RNA-seq DEG Analysis

Report spreadsheet, DESeq2 table or count matrix → DEG selection → volcano, heatmap, PCA, Venn → Excel, PPT, DAVID/GSEA input files
Free · runs entirely in your browser

Load data

📂 Drop files or folders here, or click to choose — several at once is fine
Report spreadsheets, CSV/TSV · per-sample quantification files · BAM + GTF · FASTQ (.gz) — file types are detected automatically
① Sequencing-service report spreadsheetSection titles such as Fold change · p-value · Normalized data in the first row, comparisons (B/A) and sample names in the second row
② DESeq2 · edgeR · limma results tableA table with gene, log2FoldChange (logFC), pvalue and padj (FDR) columns — one comparison
③ Count matrix (raw counts / TPM)Genes in the first column, samples in the rest. Groups are formed by dropping the replicate number (_1, -2, rep3) from sample names, and p-values are calculated
④ Per-sample quantification files (several, or whole folders)featureCounts · Salmon (quant.sf) · kallisto · RSEM · STAR (ReadsPerGene) · HTSeq outputs are merged into one count matrix automatically
⑤ BAM + GTFDrop aligned BAMs with a gene annotation (GTF) — reads are counted per gene in your browser and analyzed right away (strandedness detected automatically)
⑥ FASTQ (Illumina · MGI)Identifies the sequencer and checks quality (Q30, adapters, GC, duplication), with next steps for getting expression values

DEG criteria

More settings
Barely expressed genes can show large but meaningless fold changes, so they are excluded. 1 ≈ normalized value (CPM etc.) of 1. 0 turns it off.
What do these criteria mean?
2-fold change: genes that at least double (up) or drop to half or less (down) versus the control. ±1 in log₂FC.
p-value < 0.05: the cut-off most sequencing-service reports use.
FDR: corrects for chance positives when tens of thousands of genes are tested at once. It is stricter, so you get fewer DEGs, and reviewers often ask for it.
Without replicates (one sample per group) no p-value can be calculated, so genes are selected by fold change only.

Filter by gene set

Use this to look only at a list of genes you care about or the genes in a pathway.

DEG list

Export

DEG table

Genes selected with the current criteria, with fold change, p-values and mean expression

Gene list for functional analysis

Gene names only, one per line. Paste into DAVID, Enrichr or g:Profiler for GO and pathway analysis

DAVID · Enrichr · g:Profiler (new tab)

GSEA input files

Expression of all genes for the two groups in the current comparison (.gct) plus sample labels (.cls). Three or more replicates per group recommended

KEGG Mapper color file

Entrez IDs with up (red) and down (blue) colors. Paste into KEGG Mapper – Color

KEGG Mapper – Color (new tab)

Slides

A PowerPoint file with every available chart (one per slide)

Calculating…