rnaseq-standard-flow
End-to-end umbrella route for reference or explicit de novo mode.
有参或显式无参模式的一站式总流程。
Flow Manuals流程手册
Use each RNA-seq flow alone or as part of the route
单独使用或串联使用每个 RNA-seq 流程
These manuals explain how each flow is used, how its inputs are prepared, which parameters matter, and how its outputs connect to the next flow. Reference and de novo routes are documented side by side.
这些手册说明每个流程如何使用、输入如何准备、关键参数如何选择，以及输出如何接到下一个流程。有参和无参路线并列维护。
rnaseq-index-flow
Reference preparation, transcript extraction, and index construction.
参考整理、转录本提取和索引构建。
rnaseq-expression-flow
Reference FASTQ QC, Salmon quantification, tximport, and expression matrices.
有参 FASTQ 质控、Salmon 定量、tximport 和表达矩阵。
rnaseq-denovo-assembly-flow
FASTQ QC, Trinity-first assembly, transcript filtering, assembly stats, and optional BUSCO.
FASTQ 质控、Trinity-first 组装、转录本过滤、组装统计和可选 BUSCO。
rnaseq-denovo-expression-flow
Salmon quantification against assembled transcripts and transcript-level matrices.
基于组装转录本的 Salmon 定量和转录本层面矩阵。
rnaseq-denovo-annotation-flow
ORF prediction, DIAMOND homology annotation, and optional GO-derived GMT/background.
ORF 预测、DIAMOND 同源注释，以及可选 GO 派生 GMT/background。
rnaseq-de-flow
DESeq2 differential expression and diagnostic plots for gene or transcript count matrices.
针对基因或转录本计数矩阵的 DESeq2 差异表达和诊断图。
rnaseq-enrichment-flow
Offline GMT-based ORA/GSEA enrichment and pathway-level summaries.
基于离线 GMT 的 ORA/GSEA 富集和通路层面摘要。
rnaseq-alignment-flow
Optional HISAT2 genome alignment and sorted BAM delivery.
可选 HISAT2 基因组比对和排序 BAM 输出。
rnaseq-count-flow
featureCounts gene count matrix from alignment BAM files.
从比对 BAM 生成 featureCounts 基因计数矩阵。
rnaseq-alignment-qc-flow
SAMtools, RSeQC, Qualimap, and MultiQC alignment-level QC.
SAMtools、RSeQC、Qualimap 和 MultiQC 比对层面质控。
rnaseq-report-flow
Static bilingual report collection, links, provenance, and interpretation guide.
静态双语报告收集、链接、溯源和解读指南。