v0.4.1

What's Changed

• Set seeds appropriately when NULL is passed to functions
• Fix lack of rounding for alevin-fry import
• Update lightning to fix critical alert by @jashapiro in #284

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

v0.4.0

What's Changed

• Update environment and docker images to R 4.4 and Bioconductor 3.19
• Create "slim" images for smaller downloads when possible
• Use a single Dockerfile and targets for more efficient building
• Reduced merge memory usage

Full Changelog: v0.3.2...v0.4.0

scpcaTools v0.3.2

What's Changed

• Add functionality to merge altExps in merge_sce_list(), including merging of colData, rowData and metadata
• Add an option to compress HDF5 files in sce_to_anndata()

Full Changelog: v0.3.1...v0.3.2

scpcaTools v0.3.1

What's Changed

• Update R to use 4.3.2
• Run tests with renv and current package versions
• Fixed some bugs in sce_to_anndata():
  • Remove objects and lists from metadata prior to converting SingleCellExperiment objects to AnnData
  • Check that SingleCellExperiment objects have > 1 cell prior to conversion to AnnData
• Add precommit to repo
• Update to Seurat v0.5.0 and use the AddMetaData() function in sce_to_seurat()

Full Changelog: v0.3.0...v0.3.1

scpcaTools v0.3.0

What's Changed

• Function for adding and combining sample metadata in SCE object
• Function to incorporate sample metadata into colData of SCE object
• Add argument for assay name to use for X in AnnData object
• Update to R 4.3 & Bioconductor 3.17
• Fail conversion to AnnData if SCE object doesn't have enough cells

Full Changelog: v0.2.3...v0.3.0

scpcaTools v0.2.3

What's Changed

• Addition of integration metrics
  • Average silhouette width (ASW)
  • Within-batch adjusted rand index (ARI)
  • iLISI

New Contributors

• @cbethell made their first contribution in #184

Full Changelog: v0.2.2...v0.2.3

scpcaTools v0.2.2

What's Changed

• Updates to QC report generation script
• Addition of automated code styling with styler
• renv package and docker updates, including addition of SingleR as preliminary support for cell type annotation

Full Changelog: v0.2.1...v0.2.2

scpcaTools v0.2.1

What's Changed

• Make UMAP plotting optional in QC report

Preliminary support for data integration including:

• Addition of merge_sce_list() to combine and merge SCE objects and
• integrate_sces() for integrating single-cell gene expression objects with fastMNNor harmony

Full Changelog: v0.2.0...v0.2.1

scpcaTools v0.2.0

What's Changed

• Store both the total read counts (unspliced and spliced reads) along with spliced only reads in SingleCellExperiment objects created from reading in Alevin, Alevin-fry, and Kallisto data
• Updates to QC Report to include filtering of low quality cells and UMAP plots
• Use fishpond::loadFry() to read in alevin-fry data
• Update to R 4.2 and Bioconductor 3.16
• Removed Matrix.utils dependency in collapse_intron_counts()

scpcaTools v0.1.9

What's Changed

• Added Functions for conversion of SCE objects

  • to AnnData in #114
  • to Seurat in #116 & #123

• Updated R tests for CI in #117

• Use temp directory for intermediate files when rendering Notebooks in #125

Full Changelog: v0.1.8...v0.1.9