v0.5.0

What's Changed

• adds support for H5AD (AnnData) output by with #90
• adds support for Snakemake 8 with in #83
• updates environments to R 4.3 and Bioc 3.18 with #86
• freshens up the Rmd output with #89
• adds a version variable to the Snakefile with #89

Specification Extensions

• configuration YAML: there is now a output_format key that takes a list, currently limited to "sce" (default) and "h5ad" (experimental).
• target definition: targets have two new (optional) keys - tx_annots_csv and gene_annots_csv
  These are exclusively used by the output_format: h5ad branch of the pipeline.

Full Changelog: v0.4.1...v0.5.0

v0.4.1

What's Changed

• updated whitelist URLs by @jpintar in #75
• updated docker image with #78
• updated annotations to include MWS and atlas information from the manuscript with #80
• README links published manuscript with #81

New Contributors

• @jpintar made their first contribution in #75

Notes

This version is at parity with the publication version with some added annotations and basic maintenance. For example, the annotations now include precomputed weights for isoforms that can be readily used to compute WUI values using scUTRboot. These include:

• wt_raw_all - uses all quantified isoforms
• wt_raw_no_ipa - uses all quantified non-IPA isoforms
• wt_atlas_all - uses subset of isoforms that were detected in the atlas analyses
• wt_atlas_no_ipa - uses subset of non-IPA isoforms that were detected in the atlas analyses

Full Changelog: v0.4.0...v0.4.1

v0.4.0

New Features

• target and barcode downloads are part of the pipeline (resolves #51)
• new exclude_unannotated_cells configuration option to export only annotated cells (resolves #59)

Bug Fixes

• URLs for 10X whitelists have been fixed (resolves #69)

Changes

• new Snakemake bounds of >=6.0,<8.0 (resolves #67, #71)
• sample IDs used in scUTRquant appear as sample_id.sq in colData of SingleCellExperiment objects (resolves #64)

scUTRquant Manuscript v2

This captures the state of the repository at version 2 of the bioRxiv manuscript.

v0.3.0

This version includes both human and mouse UTRomes, generated with updated pipelines.

scUTRquant Manuscript v1

This captures the state of scUTRquant code that was used in the bioRxiv scUTRquant manuscript v1.

Version 0.1

This version relies on mm10 UTRome v2019.05. Feature annotation (rowData) is based on GenomicRanges object derived from UTRome GTF file.