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Count Matrix
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Metadata
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Download RDS
① Count Matrix
Tab-separated text file — first column is gene IDs, remaining columns are samples
Drag & drop count file(s) here, or click to browse
Single file: full matrix (genes × samples) · Multiple files: one file per sample, merged automatically · STARReadsPerGene.out.tab files auto-detected — strandedness picker shown automatically
Single file: First column = gene identifiers; remaining columns = samples (headers become sample names).
Values must be raw integer counts (no normalisation).
Multiple files (one per sample): Each file has a gene-ID column and a counts column. Files are merged by gene ID (union); missing values filled with 0. Common tool suffixes are stripped from file names to form column headers:
gene sample1 sample2ENSG001 142 87
Multiple files (one per sample): Each file has a gene-ID column and a counts column. Files are merged by gene ID (union); missing values filled with 0. Common tool suffixes are stripped from file names to form column headers:
.rawCounts, .ReadsPerGene.out.tab (STAR), .featureCounts (featureCounts), .htseq-count / .htseq (HTSeq), .counts.
② Sample Metadata
Define experimental groups and covariates — each column becomes a variable in your DESeq2 design
Click Add Column to define a metadata variable (e.g. group, treatment)
Tip: Add at least one column such as
group or treatment.
Column names are editable — click the header to rename. Import an existing tab-delimited metadata
file with the Import Metadata button if you already have one prepared.
③ Download RDS
Generate a
.rds file ready for direct upload to DESeq2 ExploreRGenes
—
Samples
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Metadata columns
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Next step: Upload this
.rds file to
DESeq2 ExploreR —
go to New Session → Upload RDS to begin your differential expression analysis.