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Changelog

Source: NEWS.md

rsemflow 0.1.1

Fixes found by running rsemflow on real ENCODE RSEM output (validation/encode-k562-knockdown/).

  • annotation ensembl: genes are mapped only when the OrgDb returned a symbol, Entrez ID, or description. Previously, Ensembl IDs absent from the OrgDb were also reported as mapped (22,350 of 59,526 genes in the validation data).
  • enrichment gsea runs serially without a progress bar. On Windows it previously printed a progress bar and started a worker process. Results are unchanged.
  • annotation ensembl no longer prints an empty line when loading the OrgDb.
  • Added a reproducible real-data validation on ENCODE K562 PTBP1 and SRSF1 knockdowns.

rsemflow 0.1.0

First public release.

  • data import: RSEM *.genes.results import through tximport, with checks for required columns, one-to-one sample matching, and identical gene tables. sample_id is always read as text.
  • data summarize: sample- and gene-level expression summaries.
  • annotation ensembl / annotation gtf: gene annotation that keeps the original RSEM gene ID.
  • expression normalize / pca / correlation: VST, size-factor normalized counts, or log2(TPM + 1); PCA tables; sample correlation.
  • differential deseq2: metadata-driven DESeq2 with explicit formula, term, and reference levels; multi-group, numeric, interaction, simple-effect (--p-at), and LRT analyses. Coefficients are resolved from the design matrix, and full-rank designs are required.
  • enrichment gsea / gsva: preranked GSEA (fgseaMultilevel, fixed seed) and GSVA/ssGSEA scores with MSigDB (msigdbr, species-aware collection aliases) or custom GMT gene sets.
  • Genes with RSEM effective_length = 0 are handled when building DESeq2 objects.
  • Supports human and mouse data.
  • All results are TSV tables; no figures are produced.