TAFFISH RNA-seq project reportTAFFISH RNA-seq 项目报告
RNA-seq project
Generated by rnaseq-report-flow 0.2.0-r2 at 2026-05-30T18:54:20Z UTC. This static report follows the RNA-seq analysis path from reference or de novo transcriptome evidence through read QC, expression, alignment, differential expression, enrichment, methods, and provenance.本报告由 rnaseq-report-flow 0.2.0-r2 于 2026-05-30T18:54:20Z UTC 生成，按 RNA-seq 分析流程组织参考或无参转录组证据、测序质控、表达定量、比对计数、差异表达、功能富集、方法和溯源信息。
Project view项目视图
Executive Summary项目总览
Key metrics are collected from machine-readable upstream outputs. They provide a first-pass view for biologists, bioinformaticians, and collaborators before detailed interpretation.关键指标来自上游流程的机器可读结果，用于让生物学家、生信分析人员和协作者快速了解项目状态；正式生物学解释仍应结合实验设计和专业判断。
Reading layer阅读层
Open guide打开解读指南How to Read This Report如何阅读本报告
The main HTML keeps project outputs close to their biological questions. The companion guide explains the intended reading order, plot roles, and common interpretation boundaries in more detail.主 HTML 把项目结果放在对应的生物学问题下展示；配套解读指南进一步说明推荐阅读顺序、图表作用和常见解读边界。
Quality before conclusions先质控再结论
Review read quality, sample structure, mapping/count evidence, and distribution plots before interpreting DE or enrichment.在解释差异表达或富集前，先检查 reads 质量、样本结构、比对/计数证据和分布图。
Statistics before mechanism先统计再机制
DE tables and plots rank evidence for changed genes; they do not by themselves prove causal mechanisms.差异表格和图形用于排序变化基因的证据；它们本身不直接证明因果机制。
Gene sets need contextGene set 需要背景
ORA and GSEA should be read with the gene universe, ID mapping, and gene-set source in mind.解读 ORA 和 GSEA 时必须同时考虑背景基因集、ID 映射和 gene set 来源。
Reusable evidence可复用证据
Tables, plots, source links, commands, methods, and manifests are indexed so the report can be audited or reused.报告索引了表格、图片、来源链接、命令、方法和 manifest，便于审计和复用。
Biological logic生物学逻辑
Workflow and Biological Questions分析流程与生物学问题
The report is organized by the biological role of each step rather than by file type. Each module answers a specific question, from whether the reads are usable to which genes and biological processes changed.报告按每一步的生物学意义组织，而不是把文件简单堆叠。每个模块回答一个具体问题：reads 是否可靠、表达是否可比、样本是否分组清楚、哪些基因变化、哪些功能过程受影响。
FASTQ readsFASTQ readsraw sequencing data原始测序数据
->
QC and trimming质控与修剪read reliabilityreads 可靠性
->
Quantification表达定量gene and transcript abundance基因/转录本丰度
->
DE analysis差异表达changed genes变化基因
->
Enrichment功能富集affected processes受影响过程
->
Report报告delivery and provenance交付与溯源
Reference参考genome and annotation基因组与注释
->
Alignment比对genome-aware BAM evidence基因组层面 BAM 证据
->
Counting计数featureCounts matrixfeatureCounts 矩阵
->
RNA-seq QCRNA-seq QCmapping and library quality比对与文库质量
The first line is the default lightweight reference expression route; the second line is the optional alignment/count evidence route. When de novo outputs are supplied, a third route records assembly, transcript-level quantification, and annotation evidence without relabeling assembled transcripts as known genes.第一行是默认轻量有参表达路线；第二行是在提供上游结果时纳入的可选比对/计数证据路线。若提供无参输出，第三条路线会记录组装、转录本层面定量和注释证据，并且不会把组装转录本误写成已知基因。
Detected upstream modules检测到的上游模块
standardprovided已提供
referenceprovided已提供
expressionprovided已提供
alignmentprovided已提供
alignment_qcprovided已提供
countprovided已提供
deprovided已提供
enrichmentprovided已提供
Input output directories输入结果目录
| Module模块 | Path路径 | Status状态 |
|---|---|---|
| standard | /home/kyhan/test/rna-seq/yeast-standard-out | provided |
| reference | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/reference | provided |
| expression | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression | provided |
| alignment | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment | provided |
| count | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/count | provided |
| alignment_qc | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc | provided |
| de | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/de | provided |
| enrichment | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/enrichment | provided |
Step 1步骤 1
Reference Preparation参考构建
This step standardizes the genome annotation, extracts transcript sequences, and builds indexes used by quantification and alignment. If reference IDs are inconsistent, every downstream result can become hard to interpret.这一步统一基因组注释、提取转录本序列，并构建定量和比对所需索引。参考序列和注释 ID 若不一致，下游结果会难以解释。
Reference summary参考摘要
| metric | value |
|---|---|
| flow | rnaseq-index-flow |
| version | 0.1.0-r1 |
| mode | genome_annotation |
| indexer | salmon |
| genome_indexer | hisat2 |
| threads | 64 |
| kmer | 31 |
| transcript_count | 11607 |
| tx2gene_rows | 11169 |
| salmon_index | yes |
| kallisto_index | no |
| hisat2_index | yes |
Genome index基因组索引
| indexer | type | status | prefix |
|---|---|---|---|
| hisat2 | genome | built | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/reference/03_results/hisat2_index/genome |
Step 2步骤 2
Read QC and Expression Quantification测序质控与表达定量
Read-level QC checks sequencing quality and preprocessing behavior. Salmon quantification estimates transcript/gene abundance for the lightweight expression route.reads 层面的 QC 用来判断测序质量和预处理是否合理；Salmon 定量给出转录本/基因表达丰度，是轻量表达路线的核心输入。
QC reports质控报告
MultiQCexpression / multiqc/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/04_reports/multiqc_report.html
Open打开FastQCexpression / fastqc_SNF2KO_01/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_01/SNF2KO_01_fastqc.html
Open打开FastQCexpression / fastqc_SNF2KO_02/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_02/SNF2KO_02_fastqc.html
Open打开FastQCexpression / fastqc_SNF2KO_03/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_03/SNF2KO_03_fastqc.html
Open打开FastQCexpression / fastqc_SNF2KO_04/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_04/SNF2KO_04_fastqc.html
Open打开FastQCexpression / fastqc_SNF2KO_05/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_05/SNF2KO_05_fastqc.html
Open打开FastQCexpression / fastqc_SNF2KO_06/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_06/SNF2KO_06_fastqc.html
Open打开FastQCexpression / fastqc_SNF2KO_07/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_07/SNF2KO_07_fastqc.html
Open打开FastQCexpression / fastqc_SNF2KO_08/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_08/SNF2KO_08_fastqc.html
Open打开FastQCexpression / fastqc_SNF2KO_09/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_09/SNF2KO_09_fastqc.html
Open打开FastQCexpression / fastqc_SNF2KO_10/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_10/SNF2KO_10_fastqc.html
Open打开FastQCexpression / fastqc_SNF2KO_11/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_11/SNF2KO_11_fastqc.html
Open打开FastQCexpression / fastqc_SNF2KO_12/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_12/SNF2KO_12_fastqc.html
Open打开FastQCexpression / fastqc_WT_01/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_01/WT_01_fastqc.html
Open打开FastQCexpression / fastqc_WT_02/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_02/WT_02_fastqc.html
Open打开FastQCexpression / fastqc_WT_03/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_03/WT_03_fastqc.html
Open打开FastQCexpression / fastqc_WT_04/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_04/WT_04_fastqc.html
Open打开FastQCexpression / fastqc_WT_05/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_05/WT_05_fastqc.html
Open打开FastQCexpression / fastqc_WT_06/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_06/WT_06_fastqc.html
Open打开FastQCexpression / fastqc_WT_07/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_07/WT_07_fastqc.html
Open打开FastQCexpression / fastqc_WT_08/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_08/WT_08_fastqc.html
Open打开FastQCexpression / fastqc_WT_09/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_09/WT_09_fastqc.html
Open打开FastQCexpression / fastqc_WT_10/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_10/WT_10_fastqc.html
Open打开FastQCexpression / fastqc_WT_11/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_11/WT_11_fastqc.html
Open打开FastQCexpression / fastqc_WT_12/home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_12/WT_12_fastqc.html
Open打开Expression summary表达定量摘要
| sample_id | layout |
|---|---|
| SNF2KO_01 | false |
| SNF2KO_02 | false |
| SNF2KO_03 | false |
| SNF2KO_04 | false |
| SNF2KO_05 | false |
| SNF2KO_06 | false |
| SNF2KO_07 | false |
| SNF2KO_08 | false |
| SNF2KO_09 | false |
| SNF2KO_10 | false |
| SNF2KO_11 | false |
| SNF2KO_12 | false |
| WT_01 | false |
| WT_02 | false |
| WT_03 | false |
| WT_04 | false |
| WT_05 | false |
| WT_06 | false |
| WT_07 | false |
| WT_08 | false |
Showing 20 of 24 rows.
Quant files定量文件
| sample | file |
|---|---|
| SNF2KO_01 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/SNF2KO_01/quant.sf |
| SNF2KO_02 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/SNF2KO_02/quant.sf |
| SNF2KO_03 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/SNF2KO_03/quant.sf |
| SNF2KO_04 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/SNF2KO_04/quant.sf |
| SNF2KO_05 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/SNF2KO_05/quant.sf |
| SNF2KO_06 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/SNF2KO_06/quant.sf |
| SNF2KO_07 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/SNF2KO_07/quant.sf |
| SNF2KO_08 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/SNF2KO_08/quant.sf |
| SNF2KO_09 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/SNF2KO_09/quant.sf |
| SNF2KO_10 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/SNF2KO_10/quant.sf |
| SNF2KO_11 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/SNF2KO_11/quant.sf |
| SNF2KO_12 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/SNF2KO_12/quant.sf |
| WT_01 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/WT_01/quant.sf |
| WT_02 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/WT_02/quant.sf |
| WT_03 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/WT_03/quant.sf |
| WT_04 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/WT_04/quant.sf |
| WT_05 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/WT_05/quant.sf |
| WT_06 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/WT_06/quant.sf |
| WT_07 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/WT_07/quant.sf |
| WT_08 | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/salmon/WT_08/quant.sf |
Showing 20 of 24 rows.
Optional evidence branch可选证据分支
Alignment, Counting, and RNA-seq QC比对、计数与 RNA-seq 质控
The alignment branch provides genome-aware evidence, coordinate-sorted BAM files, featureCounts gene counts, and BAM/RNA-seq QC. It is useful for inspecting mapping quality, annotation compatibility, and count-based analyses.比对分支提供基因组层面的证据、排序 BAM、featureCounts 基因计数和 BAM/RNA-seq 质控，适合检查比对质量、注释兼容性和计数路线结果。
Alignment and QC reports比对与 QC 报告
MultiQCalignment / multiqc/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment/04_reports/multiqc_report.html
Open打开MultiQCcount / multiqc/home/kyhan/test/rna-seq/yeast-standard-out/03_results/count/04_reports/multiqc_report.html
Open打开MultiQCalignment_qc / multiqc/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/04_reports/multiqc_report.html
Open打开Qualimapalignment_qc / qualimap_SNF2KO_01/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/SNF2KO_01/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_SNF2KO_02/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/SNF2KO_02/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_SNF2KO_03/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/SNF2KO_03/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_SNF2KO_04/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/SNF2KO_04/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_SNF2KO_05/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/SNF2KO_05/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_SNF2KO_06/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/SNF2KO_06/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_SNF2KO_07/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/SNF2KO_07/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_SNF2KO_08/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/SNF2KO_08/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_SNF2KO_09/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/SNF2KO_09/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_SNF2KO_10/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/SNF2KO_10/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_SNF2KO_11/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/SNF2KO_11/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_SNF2KO_12/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/SNF2KO_12/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_WT_01/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/WT_01/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_WT_02/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/WT_02/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_WT_03/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/WT_03/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_WT_04/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/WT_04/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_WT_05/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/WT_05/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_WT_06/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/WT_06/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_WT_07/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/WT_07/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_WT_08/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/WT_08/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_WT_09/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/WT_09/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_WT_10/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/WT_10/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_WT_11/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/WT_11/qualimapReport.html
Open打开Qualimapalignment_qc / qualimap_WT_12/home/kyhan/test/rna-seq/yeast-standard-out/03_results/alignment_qc/03_results/qualimap/WT_12/qualimapReport.html
Open打开Alignment summary比对摘要
| sample_id | layout | trimmed | total_reads | mapped_reads |
|---|---|---|---|---|
| SNF2KO_01 | single-end | false | 557797 | 543970 |
| SNF2KO_02 | single-end | false | 594380 | 577772 |
| SNF2KO_03 | single-end | false | 555987 | 539684 |
| SNF2KO_04 | single-end | false | 631104 | 622238 |
| SNF2KO_05 | single-end | false | 565903 | 548731 |
| SNF2KO_06 | single-end | false | 559767 | 542261 |
| SNF2KO_07 | single-end | false | 560921 | 542795 |
| SNF2KO_08 | single-end | false | 579664 | 560903 |
| SNF2KO_09 | single-end | false | 560351 | 544174 |
| SNF2KO_10 | single-end | false | 558763 | 542591 |
| SNF2KO_11 | single-end | false | 559476 | 539804 |
| SNF2KO_12 | single-end | false | 555036 | 539913 |
| WT_01 | single-end | false | 579070 | 560958 |
| WT_02 | single-end | false | 584415 | 569328 |
| WT_03 | single-end | false | 580298 | 559977 |
| WT_04 | single-end | false | 578664 | 564465 |
| WT_05 | single-end | false | 582829 | 567324 |
| WT_06 | single-end | false | 572391 | 559848 |
| WT_07 | single-end | false | 578018 | 563007 |
| WT_08 | single-end | false | 583945 | 568556 |
Showing 20 of 24 rows.
Count summary计数摘要
| metric | value |
|---|---|
| sample_count | 24 |
| gene_count | 7095 |
| assigned_reads | 8175143 |
| strand | 0 |
| paired | false |
| feature_type | exon |
| attribute | gene_id |
| min_mapq | 0 |
| filled_missing_attribute | 2 |
RNA-seq QC summaryRNA-seq 质控摘要
| sample_id | total_records | unique_mapq_ge_cut | mapped_reads | mapped_pct | assigned_tags |
|---|---|---|---|---|---|
| SNF2KO_01 | 557797 | mapq_cut | 543970 | 97.52 | 480664 |
| SNF2KO_02 | 594380 | mapq_cut | 577772 | 97.21 | 478315 |
| SNF2KO_03 | 555987 | mapq_cut | 539684 | 97.07 | 480968 |
| SNF2KO_04 | 631104 | mapq_cut | 622238 | 98.60 | 484317 |
| SNF2KO_05 | 565903 | mapq_cut | 548731 | 96.97 | 477431 |
| SNF2KO_06 | 559767 | mapq_cut | 542261 | 96.87 | 478137 |
| SNF2KO_07 | 560921 | mapq_cut | 542795 | 96.77 | 476173 |
| SNF2KO_08 | 579664 | mapq_cut | 560903 | 96.76 | 476499 |
| SNF2KO_09 | 560351 | mapq_cut | 544174 | 97.11 | 480495 |
| SNF2KO_10 | 558763 | mapq_cut | 542591 | 97.11 | 482236 |
| SNF2KO_11 | 559476 | mapq_cut | 539804 | 96.48 | 475637 |
| SNF2KO_12 | 555036 | mapq_cut | 539913 | 97.28 | 479497 |
| WT_01 | 579070 | mapq_cut | 560958 | 96.87 | 477752 |
| WT_02 | 584415 | mapq_cut | 569328 | 97.42 | 480795 |
| WT_03 | 580298 | mapq_cut | 559977 | 96.50 | 477225 |
| WT_04 | 578664 | mapq_cut | 564465 | 97.55 | 480149 |
| WT_05 | 582829 | mapq_cut | 567324 | 97.34 | 478205 |
| WT_06 | 572391 | mapq_cut | 559848 | 97.81 | 482731 |
| WT_07 | 578018 | mapq_cut | 563007 | 97.40 | 480465 |
| WT_08 | 583945 | mapq_cut | 568556 | 97.36 | 481217 |
Showing 20 of 24 rows.
Statistical contrast统计比较
Differential Expression差异表达
This section asks which genes change between conditions. It first checks whether samples and expression distributions are trustworthy, then presents gene-level statistical evidence and candidate expression patterns.本节回答不同条件之间哪些基因发生变化。报告会先检查样本关系和表达分布是否可信，再展示基因层面的统计证据与候选基因表达模式。
Count matrix计数矩阵genes by samples基因 x 样本
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Design and contrast设计与比较condition model条件模型
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DESeq2statistics and shrinkage统计检验与收缩
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DE genes差异基因ranked evidence排序证据
Sample structure and distributions样本结构与数据分布
These plots are quality and design checks for the statistical model: PCA and correlation show sample relationships, while expression/count distributions show whether normalization and filtering produced comparable samples.这些图用于检查统计模型的前提：PCA 和相关性展示样本关系，表达/计数分布用于判断归一化与过滤后样本是否可比。
Reviews expression/count distribution before interpreting DE results.在解读差异表达前检查表达量或计数分布。
Reviews expression/count distribution before interpreting DE results.在解读差异表达前检查表达量或计数分布。
Shows whether biological groups separate and whether outlier samples need review.查看实验组是否分离、是否存在离群样本。
Checks replicate similarity and global sample relationships.检查重复样本一致性和整体样本关系。
Differential expression signal差异表达信号
These figures summarize the actual contrast: volcano and MA plots combine effect size with uncertainty, DEG counts show the threshold-level balance, and heatmap/top-gene plots make representative expression patterns inspectable.这些图展示真正的组间比较结果：火山图和 MA 图结合效应量与不确定性，差异基因数量图展示阈值下的方向平衡，热图和 Top 基因图帮助查看代表性表达模式。
Summarizes up- and down-regulated gene counts under the selected thresholds.汇总阈值下上调和下调基因数量。
Shows expression patterns of selected variable or DE genes across samples.展示代表性基因在样本间的表达模式。
Shows fold-change behavior across mean expression levels.查看不同表达水平上的倍数变化趋势。
Makes high-impact DE genes easier to inspect by sample group.便于按样本组查看重点差异基因表达。
Combines effect size and significance to highlight candidate DE genes.同时展示效应量和显著性，突出候选差异基因。
DE summary差异表达摘要
| metric | value |
|---|---|
| flow | rnaseq-de-flow |
| version | 0.1.0-r2 |
| samples | 24 |
| input_genes | 7095 |
| tested_genes | 5780 |
| significant_genes | 367 |
| up_genes | 135 |
| down_genes | 232 |
| padj_cutoff | 0.05 |
| lfc_cutoff | 1 |
| fit_type | parametric |
| lfc_shrink | none |
| contrast | condition:snf2_KO:WT |
Standard run summarystandard-flow 摘要
No table available.
Top DESeq2 rowsDESeq2 结果预览
| gene_id | baseMean | log2FoldChange | lfcSE | stat | pvalue | padj |
|---|---|---|---|---|---|---|
| YDR033W | 220.243380003241 | -3.744395043332 | 0.108698512920816 | -34.4475277785971 | 4.90359991494182e-260 | 2.72394975275018e-256 |
| YOR153W | 342.121293800372 | -2.67582407807163 | 0.0817262234812336 | -32.7413156278543 | 4.03603408862231e-235 | 1.12100846811485e-231 |
| YGR234W | 126.045989486502 | -4.17291016044632 | 0.132585883507382 | -31.4732613311279 | 2.01766134597011e-217 | 3.73603625895466e-214 |
| YER081W | 185.448547639219 | 3.10169555625315 | 0.10727765156635 | 28.9127838926898 | 8.24702896868883e-184 | 1.14530614802666e-180 |
| YDR077W | 1363.75272198537 | -3.50973267733247 | 0.124121625204988 | -28.2765607647829 | 6.71242748595142e-176 | 7.45750693689202e-173 |
| YPL019C | 99.7651283242153 | -2.49080210578036 | 0.102039122314365 | -24.4102658792636 | 1.33061420639487e-131 | 1.23192698608725e-128 |
| YPR149W | 166.878298086628 | -2.18497472421615 | 0.0898659836265275 | -24.3137017594628 | 1.40424467009952e-130 | 1.11436844891469e-127 |
| YHR092C | 388.463412109091 | -2.48538010621361 | 0.113386886692229 | -21.9194668688611 | 1.69429860305204e-106 | 1.17647859249426e-103 |
| YBR067C | 201.474387021906 | -2.80468395566298 | 0.131356884095394 | -21.3516328053744 | 3.7655031714127e-101 | 2.32415223524417e-98 |
| YFR015C | 287.328114826962 | -3.05847684775855 | 0.146430973720218 | -20.8868162934046 | 7.05698455665219e-97 | 3.92015492122029e-94 |
| YOR273C | 101.202179768018 | -2.03717358920145 | 0.0980086064004914 | -20.7856601988296 | 5.83560503291303e-96 | 2.94698054162108e-93 |
| YER011W | 66.1124564360921 | -3.85101714042377 | 0.190246604175293 | -20.2422385257161 | 4.158459101995e-91 | 1.92502002596519e-88 |
| YOL109W | 135.185071754148 | -2.47960702802368 | 0.125112973420931 | -19.8189441128641 | 2.04351369877618e-87 | 8.73209122823205e-85 |
| YKL109W | 86.1256443833836 | -1.86139347585598 | 0.0950188093590803 | -19.5897368995827 | 1.89165253459414e-85 | 7.50580702119316e-83 |
| YIL121W | 44.5877718277696 | -2.66758577169715 | 0.138708479076251 | -19.2315984535504 | 2.01326206485439e-82 | 7.45578051351077e-80 |
| YDR406W | 72.2271908703235 | -2.02866403522397 | 0.1058593357909 | -19.1637706780167 | 7.429115239447e-82 | 2.5792959471955e-79 |
| YCL064C | 150.339699789093 | -1.39085752654853 | 0.0770508785524561 | -18.0511572700841 | 7.72549184881603e-73 | 2.38417262334295e-70 |
| YDL039C | 73.9697102269784 | -3.19405104489321 | 0.176922108861269 | -18.0534307749959 | 7.41391272302737e-73 | 2.38417262334295e-70 |
| YEL071W | 183.455791937845 | 1.13055060121924 | 0.0626939079447475 | 18.0328621756296 | 1.07576126066951e-72 | 3.14518621211533e-70 |
| YJL012C | 116.327260403508 | -1.38408654454497 | 0.0789925322364674 | -17.5217391487292 | 9.77898032284681e-69 | 2.7161117846707e-66 |
Showing 20 of 5780 rows.
Biological interpretation layer生物学解释层
Functional Enrichment功能富集
Enrichment analysis groups changed genes into biological processes or gene sets, helping move from a gene list to biological hypotheses. The displayed terms should be interpreted with the selected background and gene-set source in mind.富集分析把差异基因组织到生物过程或基因集合中，帮助从基因列表走向生物学假设。解读这些条目时必须同时考虑背景基因集合和 gene set 来源。
DE genes差异基因ORA
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Over-represented sets过度代表集合term-level hypothesis条目层面假设
Ranked genes排序基因GSEA
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Directional signals方向性信号pathway-like trend通路式趋势
ORA visual summaryORA 可视化摘要
ORA starts from the significant-gene list and asks which gene sets contain more hits than expected under the selected background universe. The readable dotplot is the primary review figure, the classic dotplot preserves a familiar audit view, and the barplot emphasizes the strongest term-level signals.ORA 从显著差异基因列表出发，检验在选定背景基因集中哪些 gene set 命中数高于随机期望。可读气泡图是主要查看图，经典气泡图保留常见审计视图，柱状图突出最强的条目层面信号。
Summarizes enriched biological processes with wrapped readable labels.用换行后的可读标签展示富集生物过程。
Preserves the classic enrichment view with improved canvas sizing for audit.保留经典富集视图，并优化画布尺寸以便审计。
Ranks top over-represented gene sets by significance while showing term-level signal.按显著性展示 ORA Top 基因集合，便于快速查看条目强度。
GSEA directional summaryGSEA 方向性摘要
GSEA uses the ranked gene list rather than a hard significant-gene cutoff. NES plots compare positive and negative enrichment directions, while running curves show where representative gene-set members accumulate along the ranked evidence list.GSEA 使用排序基因列表，而不是只看显著基因阈值。NES 图比较正向和负向富集强度，running curve 展示代表性 gene set 成员在排序证据列表中的累积位置。
Displays running enrichment curves for representative GSEA gene sets.展示代表性 GSEA gene set 的 running enrichment 曲线。
Shows the strongest positive and negative normalized enrichment scores from preranked GSEA.展示 preranked GSEA 中正向和负向最强的标准化富集分数。
Enrichment summary富集摘要
| metric | value |
|---|---|
| app | enrichment-r |
| version | 0.1.0 |
| gene_sets_total | 2274 |
| gene_list_count | 354 |
| ranked_gene_count | 5660 |
| background_count | 7127 |
| background_source | background.tsv |
| ora_result_count | 304 |
| gsea_result_count | 1428 |
| plot_source | ora |
Interpretation boundary解读边界
This flow reports offline GMT-based ORA/GSEA outputs produced upstream. Gene set source, ID space, background universe, and biological interpretation remain project decisions.本流程只汇总上游基于离线 GMT 的 ORA/GSEA 结果。gene set 来源、ID 空间、背景基因集和最终生物学解释仍属于项目决策。
This flow reports offline GMT-based ORA/GSEA outputs produced upstream. Gene set source, ID space, background universe, and biological interpretation remain project decisions.本流程只汇总上游基于离线 GMT 的 ORA/GSEA 结果。gene set 来源、ID 空间、背景基因集和最终生物学解释仍属于项目决策。
Top ORA rowsORA 结果预览
| ID | Description | GeneRatio | BgRatio | pvalue | p.adjust | qvalue | geneID |
|---|---|---|---|---|---|---|---|
| GO:0006364 | rRNA processing [biological_process] | 14/354 | 72/7127 | 9.26895068134009e-06 | 0.00281776100712739 | 0.00281776100712739 | YCR018C/YDL229W/YDR299W/YDR412W/YGR159C/YHR062C/YHR085W/YHR148W/YHR197W/YKL009W/YLL008W/YNL112W/YNL182C/YPL093W |
| GO:0006796 | phosphate-containing compound metabolic process [biological_process] | 4/354 | 5/7127 | 2.87686836796521e-05 | 0.00311932053231178 | 0.00311932053231178 | YAR071W/YBR092C/YBR093C/YGR233C |
| GO:0008645 | hexose transmembrane transport [biological_process] | 6/354 | 14/7127 | 3.07827684109715e-05 | 0.00311932053231178 | 0.00311932053231178 | YDR342C/YDR343C/YDR345C/YHR092C/YJL219W/YOL156W |
| GO:0006799 | polyphosphate biosynthetic process [biological_process] | 3/354 | 3/7127 | 0.000121557899069488 | 0.00706405074127965 | 0.00706405074127965 | YDR089W/YER072W/YJL012C |
| GO:0031505 | fungal-type cell wall organization [biological_process] | 13/354 | 80/7127 | 0.000137160169504721 | 0.00706405074127965 | 0.00706405074127965 | YBR067C/YDR055W/YDR077W/YDR528W/YEL040W/YER011W/YIR039C/YKL096W/YKL163W/YLR194C/YLR300W/YOL109W/YOL155C |
| GO:0000920 | septum digestion after cytokinesis [biological_process] | 6/354 | 18/7127 | 0.000160576806999331 | 0.00706405074127965 | 0.00706405074127965 | YCR057C/YER124C/YHR143W/YLR286C/YNL327W/YNR067C |
| GO:0006730 | one-carbon metabolic process [biological_process] | 4/354 | 7/7127 | 0.000185896072138938 | 0.00706405074127965 | 0.00706405074127965 | YAL044C/YDR019C/YKR080W/YLR058C |
| GO:1904659 | D-glucose transmembrane transport [biological_process] | 4/354 | 7/7127 | 0.000185896072138938 | 0.00706405074127965 | 0.00706405074127965 | YDR277C/YDR342C/YDR345C/YMR011W |
| GO:0005978 | glycogen biosynthetic process [biological_process] | 4/354 | 9/7127 | 0.000617931133321826 | 0.020872340503315 | 0.020872340503315 | YFR015C/YKR058W/YLR258W/YMR105C |
| GO:0006189 | 'de novo' IMP biosynthetic process [biological_process] | 3/354 | 6/7127 | 0.00217209561841506 | 0.0660317067998179 | 0.0660317067998179 | YAR015W/YMR120C/YMR300C |
| GO:0030174 | regulation of DNA-templated DNA replication initiation [biological_process] | 4/354 | 15/7127 | 0.00527859055149416 | 0.107045161819315 | 0.107045161819315 | YHR085W/YHR197W/YJL194W/YNL182C |
| GO:0000462 | maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [biological_process] | 9/354 | 67/7127 | 0.00553766083189876 | 0.107045161819315 | 0.107045161819315 | YCR057C/YDR299W/YGR128C/YHR196W/YIL091C/YKL078W/YKR060W/YMR093W/YOR004W |
| GO:0015891 | siderophore transport [biological_process] | 3/354 | 8/7127 | 0.00564444386873736 | 0.107045161819315 | 0.107045161819315 | YEL065W/YHL047C/YOR383C |
| GO:0006144 | purine nucleobase metabolic process [biological_process] | 2/354 | 3/7127 | 0.00713841855586759 | 0.107045161819315 | 0.107045161819315 | YGL234W/YOR128C |
| GO:0006650 | glycerophospholipid metabolic process [biological_process] | 2/354 | 3/7127 | 0.00713841855586759 | 0.107045161819315 | 0.107045161819315 | YMR006C/YMR008C |
| GO:0007009 | plasma membrane organization [biological_process] | 2/354 | 3/7127 | 0.00713841855586759 | 0.107045161819315 | 0.107045161819315 | YFL014W/YPR149W |
| GO:0009636 | response to toxic substance [biological_process] | 2/354 | 3/7127 | 0.00713841855586759 | 0.107045161819315 | 0.107045161819315 | YGR177C/YOL002C |
| GO:0033499 | galactose catabolic process via UDP-galactose, Leloir pathway [biological_process] | 2/354 | 3/7127 | 0.00713841855586759 | 0.107045161819315 | 0.107045161819315 | YBR018C/YBR019C |
| GO:0035435 | phosphate ion transmembrane transport [biological_process] | 2/354 | 3/7127 | 0.00713841855586759 | 0.107045161819315 | 0.107045161819315 | YBR296C/YER053C |
| GO:0071218 | cellular response to misfolded protein [biological_process] | 2/354 | 3/7127 | 0.00713841855586759 | 0.107045161819315 | 0.107045161819315 | YGR234W/YJL082W |
Showing 20 of 304 rows.
Top GSEA rowsGSEA 结果预览
| ID | Description | pvalue | p.adjust | ES | NES | size | leadingEdge |
|---|---|---|---|---|---|---|---|
| GO:0002181 | cytoplasmic translation [biological_process] | 6.37515806760749e-17 | 9.10372572054349e-14 | -0.713639685899654 | -2.46713090334951 | 119 | YDL229W/YER131W/YJL177W/YMR242C/YHR064C/YML026C/YHL033C/YLR048W/YKL056C/YNL209W/YPL198W/YNL069C/YPL131W/YGR214W/YIL018W/YBL087C/YMR142C/YFR031C-A/YPL079W/YLR264W/YKL180W/YOR091W/YJL190C/YNL301C/YER056C-A/YDR450W/YGL147C/YDR471W/YLR344W/YBR031W/YIL069C/YBR261C/YDL075W/YBL027W/YDL136W/YCR031C/YOL120C/YBL092W/YGL076C/YKR094C/YDR152W/YOR293W/YLL045C/YLR406C/YLR441C/YJR145C/YIL148W/YIL133C/YIL052C/YBR084C-A/YDL191W/YDL061C/YMR230W/YNL178W/YEL054C/YML063W/YFL034C-A/YPR163C/YGR173W/YOR234C/YLR388W/YDR500C/YOR312C/YHR141C/YHR010W/YHR203C/YHL001W/YJR094W-A/YER117W/YOR096W/YLR029C/YOL039W/YNL067W/YOL127W/YNL162W/YGL135W/YGR034W/YER074W/YLR075W/YNL096C/YLR333C/YDL130W/YLR448W/YBR061C/YDR447C/YML024W/YDL081C/YJL191W/YGR085C/YLR340W/YPR102C |
| GO:0006364 | rRNA processing [biological_process] | 2.16913947792308e-11 | 1.54876558723708e-08 | -0.740512337791809 | -2.34754184567824 | 68 | YDL229W/YCR018C/YHR064C/YGR159C/YPL093W/YHR062C/YNL209W/YKL009W/YNL112W/YDL014W/YHR197W/YNL221C/YGL120C/YLL008W/YOR063W/YNL182C/YLR175W/YJL033W/YKL172W/YDR365C/YDR299W/YHR085W/YLR196W/YHR148W/YLR409C/YPR016C/YDL208W/YEL055C/YGR285C/YPL082C/YGR090W/YLR197W/YLR106C/YMR049C/YDR087C/YMR290C/YBR247C/YDL148C/YNL075W/YPL235W/YMR239C/YDR412W/YAL033W/YOL080C/YOR287C/YLL035W/YLR002C/YPR144C |
| GO:0000462 | maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [biological_process] | 5.14510590236174e-10 | 2.44907040952419e-07 | -0.727768899899582 | -2.3000508072689 | 66 | YCR057C/YBR189W/YGR128C/YDR064W/YDR398W/YLR222C/YOR004W/YDL060W/YGL120C/YIL091C/YPL126W/YIL069C/YDR299W/YHL015W/YCR031C/YMR093W/YGR103W/YPL012W/YLR129W/YOR056C/YDR025W/YMR128W/YLR441C/YER082C/YHR196W/YJL109C/YPL090C/YGR145W/YOR119C/YBR048W/YKL078W/YAL035W/YKR060W/YDL153C/YER102W/YML063W/YKL156W/YHR065C/YHR021C/YLL011W/YDR324C/YBL072C/YLR435W/YMR290C/YDL148C/YGR118W/YBR181C/YDR449C/YOR287C/YER074W/YGR271C-A/YPR132W/YDL166C/YJL191W |
| GO:0042273 | ribosomal large subunit biogenesis [biological_process] | 1.6379849503933e-09 | 5.84760627290409e-07 | -0.770961446186613 | -2.28338099306598 | 46 | YPL093W/YKL009W/YPL198W/YFR031C-A/YNR046W/YAL025C/YGR162W/YPL211W/YGL120C/YGR103W/YOR206W/YGL076C/YBR267W/YDL063C/YNL061W/YLR397C/YOR272W/YIR012W/YPR016C/YDR091C/YLR009W/YLL034C/YGL111W/YGR245C/YDR060W/YNL002C/YER002W/YOR294W/YMR049C/YDR496C/YER126C/YBR142W/YMR290C/YNL110C/YDR161W/YPL043W |
| GO:0000447 | endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [biological_process] | 2.04403855559969e-08 | 5.83777411479272e-06 | -0.757286158562324 | -2.22530568554461 | 43 | YML026C/YLR048W/YCR057C/YGR214W/YLR222C/YOR004W/YHR169W/YDR450W/YJR002W/YML093W/YLR129W/YER082C/YER127W/YPR112C/YJL109C/YGL171W/YJL069C/YDL153C/YMR229C/YKR057W/YOL010W/YOR294W/YJL010C/YJL136C/YNR054C/YPR137W/YBR247C/YDL148C/YKL099C/YOR145C/YDR449C/YPR144C/YDR339C/YLR186W/YBL004W/YLR051C/YNL308C |
| GO:0000463 | maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [biological_process] | 6.43122403352177e-07 | 0.000153063131997818 | -0.759691122205025 | -2.14005217476478 | 34 | YER131W/YAL025C/YLR276C/YPL211W/YGL120C/YHR052W/YDL136W/YHR085W/YNL061W/YKR024C/YPR016C/YHR088W/YDL191W/YNR038W/YER006W/YNL002C/YCL054W/YER126C/YLR435W/YBR142W/YMR290C/YNL110C/YHR066W/YPL043W/YKL014C/YKR081C/YDL031W/YOL041C |
| GO:0000027 | ribosomal large subunit assembly [biological_process] | 1.08330454426229e-06 | 0.000220994127029507 | -0.744481912283062 | -2.12254835726187 | 36 | YPL131W/YHR197W/YOL077C/YLL008W/YOR063W/YNL182C/YKR094C/YCR072C/YHR085W/YIL148W/YIR012W/YEL055C/YEL054C/YGL099W/YDR060W/YLR106C/YHL001W/YHR066W/YOL127W/YOL080C/YKR081C/YLR221C/YIL110W/YLR075W/YDR312W/YLR448W/YIR026C/YGR085C/YLR340W/YPR102C |
| GO:0000472 | endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [biological_process] | 1.95529016884311e-06 | 0.000349019295138495 | -0.753517995200394 | -2.10450947731615 | 32 | YCR057C/YLR222C/YOR004W/YHR169W/YJR002W/YML093W/YLR129W/YER082C/YPR112C/YJL109C/YGL171W/YJL069C/YDL153C/YMR229C/YOL010W/YJL010C/YNR054C/YPR137W/YDL148C/YKL099C/YOR145C/YDR449C/YPR144C/YDR339C/YLR186W/YBL004W/YLR051C/YPL217C |
| GO:0000480 | endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [biological_process] | 3.18515580301512e-06 | 0.000505378054078399 | -0.756204679921362 | -2.10338169640844 | 31 | YCR057C/YLR222C/YOR004W/YHR169W/YJR002W/YML093W/YLR129W/YER082C/YER127W/YPR112C/YJL109C/YGL171W/YJL069C/YDL153C/YMR229C/YOL010W/YJL010C/YNR054C/YPR137W/YDL148C/YKL099C/YDR449C/YPR144C/YDR339C/YLR186W/YBL004W/YLR051C/YPL217C |
| GO:0031505 | fungal-type cell wall organization [biological_process] | 5.40745499841306e-06 | 0.000772184573773386 | -0.606708114043047 | -1.96900282498422 | 78 | YDR077W/YBR067C/YER011W/YOL109W/YLR300W/YDR055W/YEL040W/YOL155C/YMR307W/YKL164C/YKL096W/YIL123W/YOL061W/YJR104C/YKL163W/YLR194C/YLR120C/YKL181W/YJL158C/YKL096W-A/YJL159W |
| GO:0006096 | glycolytic process [biological_process] | 4.22799996453304e-05 | 0.00548871268123016 | -0.813329561222472 | -1.95902691447476 | 16 | YHR174W/YAL038W/YBR196C/YMR205C/YGR192C/YKL060C/YFR053C/YGL253W/YCL040W/YJL052W/YGR240C/YDR050C/YCR012W/YGR254W |
| GO:0042274 | ribosomal small subunit biogenesis [biological_process] | 9.21962102728799e-05 | 0.0109713490224727 | -0.729572742946075 | -1.97722834781245 | 27 | YPL226W/YNR046W/YNL302C/YIL091C/YOL121C/YMR014W/YHR148W/YGR145W/YKR060W/YNL132W/YMR290C/YDL148C/YPL239W/YNL075W/YOL022C/YKL143W/YOR287C/YPR144C/YLR186W |
| GO:0006839 | mitochondrial transport [biological_process] | 0.000218258100921959 | 0.0239748129320429 | 0.86457961848196 | 2.00474929769031 | 8 | YMR056C/YPL134C/YOR222W/YBL030C |
| GO:0007118 | budding cell apical bud growth [biological_process] | 0.000285487488730207 | 0.0291197238504811 | 0.704219991543776 | 2.01901602852132 | 17 | YOR127W/YBL085W/YLL021W/YNL161W/YMR200W/YNL271C/YKR020W |
| GO:0000266 | mitochondrial fission [biological_process] | 0.000360813414137708 | 0.0343494370259098 | 0.815387432866516 | 1.96209433408063 | 9 | YDR150W/YPL218W/YLL001W/YIL156W-B |
| GO:0032258 | cytoplasm to vacuole targeting by the Cvt pathway [biological_process] | 0.000410805995489779 | 0.0366644350974628 | 0.514590569459407 | 1.8702015883819 | 46 | YLR417W/YML001W/YKL103C/YML071C/YDL113C/YPR049C/YKR068C/YNL223W/YOL018C/YBL078C/YBR217W/YHR171W/YGL124C/YJL178C/YPL149W/YGL223C/YLR262C/YGL005C/YGL095C/YNL242W/YNL041C/YGL180W/YNR007C/YLR431C/YDL029W/YJL036W/YDR108W |
| GO:1904659 | D-glucose transmembrane transport [biological_process] | 0.000484660637048631 | 0.040711493512085 | -0.904896629224092 | -1.82831246155856 | 7 | YDR342C/YDR345C/YDR277C/YMR011W |
| GO:0006799 | polyphosphate biosynthetic process [biological_process] | 0.000528931684646102 | 0.0419619136485908 | -0.984090507336044 | -1.57134523502187 | 3 | YJL012C/YER072W/YDR089W |
| GO:0000742 | karyogamy involved in conjugation with cellular fusion [biological_process] | 0.000654171457766512 | 0.0491661495626621 | 0.727684204330875 | 1.97229418679731 | 14 | YMR198W/YPR141C/YNL188W/YHR073W/YCL055W/YBR109C/YDR356W/YMR065W |
| GO:0006164 | purine nucleotide biosynthetic process [biological_process] | 0.000794185934460721 | 0.0567048757204955 | -0.895488564869704 | -1.80930379168096 | 7 | YMR120C/YAR015W/YNL220W/YLR359W/YGR061C |
Showing 20 of 1428 rows.
Files to reuse可复用文件
Deliverables and Output Structure交付文件与输出结构
The report directory is designed for project delivery: the HTML is the entry point, while TSV indexes keep every copied table, plot, HTML report bundle, method record, version row, and command log auditable.报告目录面向项目交付：HTML 是入口，TSV 索引则保留每个复制的表格、图片、HTML 报告 bundle、方法、版本和命令记录，便于审计和复用。
04_reports/rnaseq_report.html
Main bilingual static report.主双语静态报告。
04_reports/report_interpretation.html
Companion guide for reading plots, biological context, and interpretation boundaries.用于阅读图表、生物学背景和解读边界的配套指南。
03_results/collected_tables/
Copied summary tables and key matrices.复制的摘要表和关键矩阵。
03_results/collected_plots/
Copied PNG/PDF plot files used by the report.报告使用的 PNG/PDF 图片副本。
03_results/collected_html/
Offline QC/report HTML bundles linked from the report.报告跳转的离线 QC/报告 HTML bundle。
04_reports/*.tsv
Machine-readable indexes, metrics, versions, and links.机器可读索引、指标、版本和链接。
run.manifest.json
Run manifest for automation and archiving.用于自动化和归档的运行 manifest。
<outdir>/ 00_inputs/upstream_outputs.tsv 01_logs/flow.log 01_logs/steps/ 03_results/collected_tables/ 03_results/collected_plots/ 03_results/collected_html/ 04_reports/rnaseq_report.html 04_reports/report_interpretation.html 04_reports/project_summary.tsv 04_reports/key_metrics.tsv 04_reports/plot_gallery.tsv 04_reports/html_reports.tsv 04_reports/tool_links.tsv 04_reports/commands.sh 04_reports/versions.tsv 04_reports/methods.txt run.manifest.json
Plot gallery index图片索引
| module | plot | png | |
|---|---|---|---|
| de | deg_counts_barplot | ../03_results/collected_plots/de.deg_counts_barplot.png | ../03_results/collected_plots/de.deg_counts_barplot.pdf |
| de | expression_distribution | ../03_results/collected_plots/de.expression_distribution.png | ../03_results/collected_plots/de.expression_distribution.pdf |
| de | heatmap | ../03_results/collected_plots/de.heatmap.png | ../03_results/collected_plots/de.heatmap.pdf |
| de | ma_plot | ../03_results/collected_plots/de.ma_plot.png | ../03_results/collected_plots/de.ma_plot.pdf |
| de | normalized_count_distribution | ../03_results/collected_plots/de.normalized_count_distribution.png | ../03_results/collected_plots/de.normalized_count_distribution.pdf |
| de | pca_plot | ../03_results/collected_plots/de.pca_plot.png | ../03_results/collected_plots/de.pca_plot.pdf |
| de | sample_correlation_heatmap | ../03_results/collected_plots/de.sample_correlation_heatmap.png | ../03_results/collected_plots/de.sample_correlation_heatmap.pdf |
| de | top_genes_expression | ../03_results/collected_plots/de.top_genes_expression.png | ../03_results/collected_plots/de.top_genes_expression.pdf |
| de | volcano_plot | ../03_results/collected_plots/de.volcano_plot.png | ../03_results/collected_plots/de.volcano_plot.pdf |
| enrichment | dotplot | ../03_results/collected_plots/enrichment.dotplot.png | ../03_results/collected_plots/enrichment.dotplot.pdf |
| enrichment | dotplot_original | ../03_results/collected_plots/enrichment.dotplot_original.png | ../03_results/collected_plots/enrichment.dotplot_original.pdf |
| enrichment | gsea_enrichment_curves | ../03_results/collected_plots/enrichment.gsea_enrichment_curves.png | ../03_results/collected_plots/enrichment.gsea_enrichment_curves.pdf |
| enrichment | gsea_nes_plot | ../03_results/collected_plots/enrichment.gsea_nes_plot.png | ../03_results/collected_plots/enrichment.gsea_nes_plot.pdf |
| enrichment | ora_barplot | ../03_results/collected_plots/enrichment.ora_barplot.png | ../03_results/collected_plots/enrichment.ora_barplot.pdf |
HTML report indexHTML 报告索引
| module | report | type | original_path | local_path | relative_path |
|---|---|---|---|---|---|
| expression | multiqc | MultiQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/04_reports/multiqc_report.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.multiqc/index.html | ../03_results/collected_html/expression.multiqc/index.html |
| expression | fastqc_SNF2KO_01 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_01/SNF2KO_01_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_SNF2KO_01/index.html | ../03_results/collected_html/expression.fastqc_SNF2KO_01/index.html |
| expression | fastqc_SNF2KO_02 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_02/SNF2KO_02_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_SNF2KO_02/index.html | ../03_results/collected_html/expression.fastqc_SNF2KO_02/index.html |
| expression | fastqc_SNF2KO_03 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_03/SNF2KO_03_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_SNF2KO_03/index.html | ../03_results/collected_html/expression.fastqc_SNF2KO_03/index.html |
| expression | fastqc_SNF2KO_04 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_04/SNF2KO_04_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_SNF2KO_04/index.html | ../03_results/collected_html/expression.fastqc_SNF2KO_04/index.html |
| expression | fastqc_SNF2KO_05 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_05/SNF2KO_05_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_SNF2KO_05/index.html | ../03_results/collected_html/expression.fastqc_SNF2KO_05/index.html |
| expression | fastqc_SNF2KO_06 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_06/SNF2KO_06_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_SNF2KO_06/index.html | ../03_results/collected_html/expression.fastqc_SNF2KO_06/index.html |
| expression | fastqc_SNF2KO_07 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_07/SNF2KO_07_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_SNF2KO_07/index.html | ../03_results/collected_html/expression.fastqc_SNF2KO_07/index.html |
| expression | fastqc_SNF2KO_08 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_08/SNF2KO_08_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_SNF2KO_08/index.html | ../03_results/collected_html/expression.fastqc_SNF2KO_08/index.html |
| expression | fastqc_SNF2KO_09 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_09/SNF2KO_09_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_SNF2KO_09/index.html | ../03_results/collected_html/expression.fastqc_SNF2KO_09/index.html |
| expression | fastqc_SNF2KO_10 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_10/SNF2KO_10_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_SNF2KO_10/index.html | ../03_results/collected_html/expression.fastqc_SNF2KO_10/index.html |
| expression | fastqc_SNF2KO_11 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_11/SNF2KO_11_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_SNF2KO_11/index.html | ../03_results/collected_html/expression.fastqc_SNF2KO_11/index.html |
| expression | fastqc_SNF2KO_12 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/SNF2KO_12/SNF2KO_12_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_SNF2KO_12/index.html | ../03_results/collected_html/expression.fastqc_SNF2KO_12/index.html |
| expression | fastqc_WT_01 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_01/WT_01_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_WT_01/index.html | ../03_results/collected_html/expression.fastqc_WT_01/index.html |
| expression | fastqc_WT_02 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_02/WT_02_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_WT_02/index.html | ../03_results/collected_html/expression.fastqc_WT_02/index.html |
| expression | fastqc_WT_03 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_03/WT_03_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_WT_03/index.html | ../03_results/collected_html/expression.fastqc_WT_03/index.html |
| expression | fastqc_WT_04 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_04/WT_04_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_WT_04/index.html | ../03_results/collected_html/expression.fastqc_WT_04/index.html |
| expression | fastqc_WT_05 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_05/WT_05_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_WT_05/index.html | ../03_results/collected_html/expression.fastqc_WT_05/index.html |
| expression | fastqc_WT_06 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_06/WT_06_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_WT_06/index.html | ../03_results/collected_html/expression.fastqc_WT_06/index.html |
| expression | fastqc_WT_07 | FastQC | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/expression/03_results/fastqc/WT_07/WT_07_fastqc.html | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_html/expression.fastqc_WT_07/index.html | ../03_results/collected_html/expression.fastqc_WT_07/index.html |
Showing 20 of 52 rows.
Report and source links open in a new browser tab to keep the main project report in place.报告和来源链接默认在新标签页打开，以便保留主项目报告位置。
Reproducibility可复现性
Tools and Source Links工具与来源链接
Tool and flow versions are collected from upstream versions.tsv files. Links point to TAFFISH wrappers or upstream project pages when known.工具和流程版本来自上游 versions.tsv。链接优先指向 TAFFISH 包装仓库或已知上游项目页面。
| Tool or flow工具或流程 | Version版本 | Recorded source记录来源 | Link链接 |
|---|---|---|---|
| rnaseq-report-flow | 0.2.0-r2 | taffish flow | source来源 |
| rnaseq-standard-flow | 0.2.0-r2 | standard:taffish flow | source来源 |
| taf-rnaseq-index-flow | 0.1.0-r1 | standard:taffish dependency | source来源 |
| taf-rnaseq-expression-flow | 0.1.0-r1 | standard:taffish dependency | source来源 |
| taf-rnaseq-alignment-flow | 0.1.0-r1 | standard:taffish dependency | source来源 |
| taf-rnaseq-alignment-qc-flow | 0.1.0-r1 | standard:taffish dependency | source来源 |
| taf-rnaseq-count-flow | 0.1.0-r1 | standard:taffish dependency | source来源 |
| taf-rnaseq-de-flow | 0.1.0-r2 | standard:taffish dependency | source来源 |
| taf-rnaseq-enrichment-flow | 0.1.0-r3 | standard:taffish dependency | source来源 |
| taf-rnaseq-report-flow | 0.2.0-r2 | standard:taffish dependency | source来源 |
| taf-rnaseq-denovo-assembly-flow | 0.1.0-r1 | standard:taffish dependency | source来源 |
| taf-rnaseq-denovo-expression-flow | 0.1.0-r1 | standard:taffish dependency | source来源 |
| taf-rnaseq-denovo-annotation-flow | 0.1.0-r1 | standard:taffish dependency | source来源 |
| rnaseq-index-flow | 0.1.0-r1 | reference:flow wrapper | source来源 |
| taf-gffread | 0.12.9-r1 | reference:annotation conversion and transcript FASTA extraction | source来源 |
| taf-agat | 1.7.0-r1 | reference:annotation normalization | source来源 |
| taf-salmon | 1.11.4-r1 | reference:Salmon transcriptome index | source来源 |
| taf-kallisto | 0.52.0-r1 | reference:optional Kallisto transcriptome index | source来源 |
| taf-hisat2 | 2.2.2-r2 | reference:optional HISAT2 genome index | source来源 |
| rnaseq-expression-flow | 0.1.0-r1 | expression:taffish flow | source来源 |
| taf-fastqc | 0.12.1-r1 | expression:taffish dependency | source来源 |
| taf-fastp | 1.3.3-r3 | expression:taffish dependency | source来源 |
| taf-multiqc | 1.35-r2 | expression:taffish dependency | source来源 |
| taf-bioconductor-rnaseq | 3.23-r1 | expression:taffish dependency | source来源 |
| rnaseq-alignment-flow | 0.1.0-r1 | alignment:taffish flow | source来源 |
| taf-samtools | 1.23.1-r1 | alignment:taffish dependency | source来源 |
| rnaseq-count-flow | 0.1.0-r1 | count:taffish flow | source来源 |
| taf-subread | 2.1.1-r2 | count:taffish dependency | source来源 |
| rnaseq-alignment-qc-flow | 0.1.0-r1 | alignment_qc:taffish flow | source来源 |
| taf-rseqc | 5.0.4-r2 | alignment_qc:taffish dependency | source来源 |
| taf-qualimap | 2.3-r1 | alignment_qc:taffish dependency | source来源 |
| rnaseq-de-flow | 0.1.0-r2 | de:taffish flow | source来源 |
| rnaseq-enrichment-flow | 0.1.0-r3 | enrichment:taffish flow | source来源 |
| taf-enrichment-r | 0.1.0-r1 | enrichment:taffish dependency | source来源 |
Audit trail审计线索
Provenance and Reuse溯源与复用
The report keeps a compact index of collected files plus full commands, methods, versions, and manifest outputs for audit and rerun context.报告保留收集文件索引、完整命令、方法描述、版本和 manifest，便于审计、复查和复现。
Report summary报告摘要
| metric | value |
|---|---|
| project_name | RNA-seq project |
| flow | rnaseq-report-flow |
| version | 0.2.0-r2 |
| started_at | 2026-05-30T18:54:18Z |
| finished_at | 2026-05-30T18:54:20Z |
| analysis_mode | reference |
| standard_out | /home/kyhan/test/rna-seq/yeast-standard-out |
| denovo_present | no |
| denovo_assembly_out | . |
| denovo_expression_out | . |
| denovo_annotation_out | . |
| provided_modules | 8 |
| collected_files | 136 |
| collected_tables | 56 |
| collected_plots | 28 |
| collected_html_reports | 52 |
| plot_groups | 14 |
| html_report_links | 52 |
Collected files收集文件
| module | role | original_path | local_path | kind | bytes |
|---|---|---|---|---|---|
| standard | methods | /home/kyhan/test/rna-seq/yeast-standard-out/04_reports/methods.txt | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_tables/standard.methods.methods.txt | table | 959 |
| standard | subflows | /home/kyhan/test/rna-seq/yeast-standard-out/04_reports/subflows.tsv | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_tables/standard.subflows.subflows.tsv | table | 782 |
| standard | plot_files | /home/kyhan/test/rna-seq/yeast-standard-out/04_reports/plot_files.tsv | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_tables/standard.plot_files.plot_files.tsv | table | 6336 |
| de | deg_counts_barplot | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/de.deg_counts_barplot.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/de.deg_counts_barplot.png | plot | 28120 |
| de | expression_distribution | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/de.expression_distribution.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/de.expression_distribution.png | plot | 112904 |
| de | heatmap | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/de.heatmap.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/de.heatmap.png | plot | 89994 |
| de | ma_plot | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/de.ma_plot.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/de.ma_plot.png | plot | 188896 |
| de | normalized_count_distribution | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/de.normalized_count_distribution.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/de.normalized_count_distribution.png | plot | 88554 |
| de | pca_plot | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/de.pca_plot.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/de.pca_plot.png | plot | 44330 |
| de | sample_correlation_heatmap | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/de.sample_correlation_heatmap.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/de.sample_correlation_heatmap.png | plot | 185166 |
| de | top_genes_expression | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/de.top_genes_expression.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/de.top_genes_expression.png | plot | 161258 |
| de | volcano_plot | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/de.volcano_plot.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/de.volcano_plot.png | plot | 98323 |
| enrichment | dotplot | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/enrichment.dotplot.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/enrichment.dotplot.png | plot | 233756 |
| enrichment | dotplot_original | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/enrichment.dotplot_original.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/enrichment.dotplot_original.png | plot | 248939 |
| enrichment | gsea_enrichment_curves | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/enrichment.gsea_enrichment_curves.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/enrichment.gsea_enrichment_curves.png | plot | 276248 |
| enrichment | gsea_nes_plot | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/enrichment.gsea_nes_plot.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/enrichment.gsea_nes_plot.png | plot | 297308 |
| enrichment | ora_barplot | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/png/enrichment.ora_barplot.png | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/enrichment.ora_barplot.png | plot | 261122 |
| de | deg_counts_barplot | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/pdf/de.deg_counts_barplot.pdf | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/de.deg_counts_barplot.pdf | plot | 4773 |
| de | expression_distribution | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/pdf/de.expression_distribution.pdf | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/de.expression_distribution.pdf | plot | 219427 |
| de | heatmap | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/plots/pdf/de.heatmap.pdf | /home/kyhan/test/rna-seq/yeast-standard-out/03_results/report/03_results/collected_plots/de.heatmap.pdf | plot | 14067 |
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Versions版本
| tool | version | source |
|---|---|---|
| rnaseq-report-flow | 0.2.0-r2 | taffish flow |
| rnaseq-standard-flow | 0.2.0-r2 | standard:taffish flow |
| taf-rnaseq-index-flow | 0.1.0-r1 | standard:taffish dependency |
| taf-rnaseq-expression-flow | 0.1.0-r1 | standard:taffish dependency |
| taf-rnaseq-alignment-flow | 0.1.0-r1 | standard:taffish dependency |
| taf-rnaseq-alignment-qc-flow | 0.1.0-r1 | standard:taffish dependency |
| taf-rnaseq-count-flow | 0.1.0-r1 | standard:taffish dependency |
| taf-rnaseq-de-flow | 0.1.0-r2 | standard:taffish dependency |
| taf-rnaseq-enrichment-flow | 0.1.0-r3 | standard:taffish dependency |
| taf-rnaseq-report-flow | 0.2.0-r2 | standard:taffish dependency |
| taf-rnaseq-denovo-assembly-flow | 0.1.0-r1 | standard:taffish dependency |
| taf-rnaseq-denovo-expression-flow | 0.1.0-r1 | standard:taffish dependency |
| taf-rnaseq-denovo-annotation-flow | 0.1.0-r1 | standard:taffish dependency |
| rnaseq-index-flow | 0.1.0-r1 | reference:flow wrapper |
| taf-gffread | 0.12.9-r1 | reference:annotation conversion and transcript FASTA extraction |
| taf-agat | 1.7.0-r1 | reference:annotation normalization |
| taf-salmon | 1.11.4-r1 | reference:Salmon transcriptome index |
| taf-kallisto | 0.52.0-r1 | reference:optional Kallisto transcriptome index |
| taf-hisat2 | 2.2.2-r2 | reference:optional HISAT2 genome index |
| rnaseq-expression-flow | 0.1.0-r1 | expression:taffish flow |
| taf-fastqc | 0.12.1-r1 | expression:taffish dependency |
| taf-fastp | 1.3.3-r3 | expression:taffish dependency |
| taf-multiqc | 1.35-r2 | expression:taffish dependency |
| taf-salmon | 1.11.4-r1 | expression:taffish dependency |
| taf-bioconductor-rnaseq | 3.23-r1 | expression:taffish dependency |
| rnaseq-alignment-flow | 0.1.0-r1 | alignment:taffish flow |
| taf-hisat2 | 2.2.2-r2 | alignment:taffish dependency |
| taf-samtools | 1.23.1-r1 | alignment:taffish dependency |
| taf-fastp | 1.3.3-r3 | alignment:taffish dependency |
| taf-multiqc | 1.35-r2 | alignment:taffish dependency |
Showing 30 of 44 rows.