Changes in version 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.

                        Changes in version 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.