BulkSeq Studio 0.15.0

BulkSeq Studio 0.15.0

Two new analysis options. Both are additive — the default pipeline (featureCounts, built-in GO/KEGG enrichment) is unchanged, and the F. graminearum DESeq2 baseline still reproduces exactly.

Added

• STAR gene-counts quantifier. With the STAR aligner, the Quantifier control is now a real choice: STAR_GeneCounts takes gene counts from STAR's own --quantMode GeneCounts output (no separate counting pass), strand-matched to the run's inferred strandedness, instead of running featureCounts. The counts converge on the same matrix the rest of the pipeline expects — validated at Pearson r ≈ 0.998 (unstranded) to 1.000 (reverse-stranded) against featureCounts on the same BAMs. featureCounts stays the default; HISAT2 uses featureCounts and Salmon uses tximport.
• Custom gene-set enrichment. Supply your own gene sets — a GMT and/or an id→term annotation table, with an optional background gene list for the over-representation universe — to run a clusterProfiler ORA + GSEA alongside the built-in GO/KEGG, producing custom ORA/GSEA tables and a dotplot. It needs no Bioconductor OrgDb, so it works even where the built-in GO route is skipped (e.g. most fungi). The gene IDs must use the run's identifier format; a namespace mismatch is flagged rather than returned as a silent empty result. The built-in GO/KEGG enrichment is unchanged.

Downloads

Windows:

• BulkSeqStudio-Setup-0.15.0.exe — installer
• BulkSeqStudio-Portable-0.15.0.zip — unzip and run BulkSeqStudio.exe, no install

Linux (x86-64, glibc 2.39+):

• BulkSeqStudio-0.15.0-x86_64.AppImage — mark executable and run
• BulkSeqStudio-linux-0.15.0.tar.gz — extract and run BulkSeqStudio