Changes in version 1.29.1                        

Reduced package size

The source tarball is now under 100 MB (94.8 MB), down from over 100 MB.
The following files were removed. All of them are archived, with the
full Salmon output for all 24 samples, on Zenodo:
https://doi.org/10.5281/zenodo.22982581. The with-inf-reps branch on
GitHub is a frozen snapshot of the package that still includes them.

  - The Gibbs inferential replicates
    (inst/extdata/quants/*/aux_info/bootstrap/, ~393 MB). tximeta() /
    tximport() on the files in inst/extdata/quants no longer imports
    inferential replicates.
  - aux_info/ambig_info.tsv.gz for each sample.
  - The full Gencode v29 GTF,
    inst/extdata/gencode.v29.annotation.gtf.gz.

New files and datasets

  - inst/extdata/gencode.v29.annotation.slim.gtf.gz: a slim Gencode v29
    GTF with only gene and transcript lines and 6 attributes (5 MB
    instead of 38 MB). It has no exon lines, so tximeta::addExons() will
    not work with it. It has a different filename from the full GTF on
    purpose: tximeta caches TxDbs by GTF filename, so this avoids
    clashing with a TxDb built from the full Gencode v29 GTF. Code that
    called makeLinkedTxome(gtf=...) with the full GTF path should switch
    to the slim filename. Built by inst/scripts/makeSlimGTF.sh.
  - data(macro_txp_se): a transcript-level SummarizedExperiment with 20
    inferential replicates, for all transcripts of 2000 random expressed
    genes plus GBP1-GBP7. The counts and infRep assays are rounded to 1
    decimal. This is now used by the fishpond swish vignette.
  - data(macro_tx2gene): a transcript-to-gene table for all Gencode v29
    transcripts, for use with tximeta::summarizeToGene(se,
    skipRanges=TRUE, tx2gene=macro_tx2gene).
  - Both datasets are built by inst/scripts/makeSumExp.R. The script
    needs a macrophage install that still has the inferential replicates
    (<= 1.29.0, or the with-inf-reps branch).

Unchanged

  - The gene-level data(gse) object and the quantification files
    (quant.sf.gz, etc.) in inst/extdata/quants are unchanged.