NEWS

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tximportData 1.41.1

Reduced package size

The package's example data has been cut from ~593 MB on disk (~388 MB compressed) to ~171 MB on disk (~96 MB compressed). The built tarball is now ~96 MiB.

The full data as it was before this change (commit 02887f7) is kept on the with-inf-reps branch and tag at https://github.com/mikelove/tximportData and archived on Zenodo: https://doi.org/10.5281/zenodo.22982575

Removed

• salmon_gibbs/: Salmon 0.8.1 output with Gibbs samples (Ensembl v87, 6 samples)
• kallisto_boot/: kallisto 0.43.0 output with bootstraps (Ensembl v87, 6 samples)
• tx2gene.ensembl.v87.csv
• gencode/gencode.v48.annotation.gtf.gz. tximeta can now link transcripts to genes with a DataFrame, so it no longer needs a GTF.
• alevin/{mouse1_unst_50,mouse1_LPS2_50}/alevin/bfh.txt and raw_cb_frequency.txt
• kallisto/*/abundance.h5 (no bootstraps). abundance.tsv.gz is kept.
• GEUVADIS samples ERR188297, ERR188329, ERR188288 and ERR188356 from kallisto/, rsem/, salmon/ and sailfish/. samples.txt and samples_extended.txt now have 2 rows: ERR188088 and ERR188021.

Kept

• salmon_ec/*/aux_info/eq_classes.txt (used by fishpond)
• alevin/mouse1_unst_50_boot/ (used by eds)
• cufflinks/, still with all 6 samples

Changes needed in downstream code

• Code that reads samples.txt now gets 2 samples instead of 6. For example, replace paste0("sample", 1:6) with paste0("sample", seq_along(files)), and replace rep(c("A","B"), each=3) with factor(c("A","B")).
• For example data with inferential replicates (Gibbs samples or bootstraps), use the Zenodo record above or another data package such as macrophage.