Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of https://github.com/alexslemonade/scpcatools

https://github.com/alexslemonade/scpcatools - v0.4.3

What's Changed

  • Fixed a bug inmerge_sce_list() to ensure the cell_id column is properly updated in the colData after merging (#299)

Full Changelog: https://github.com/AlexsLemonade/scpcaTools/compare/v0.4.2...v0.4.3

- R
Published by allyhawkins 12 months ago

https://github.com/alexslemonade/scpcatools - v0.4.2

What's Changed

  • The assays in merged objects output by merge_sce_list() were previously saved as DelayedArray, but are now saved as sparse matrices (CsparseMatrix).

Full Changelog: https://github.com/AlexsLemonade/scpcaTools/compare/v0.4.1...v0.4.2

- R
Published by allyhawkins about 1 year ago

https://github.com/alexslemonade/scpcatools - 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 https://github.com/AlexsLemonade/scpcaTools/pull/284

Full Changelog: https://github.com/AlexsLemonade/scpcaTools/compare/v0.4.0...v0.4.1

- R
Published by jashapiro over 1 year ago

https://github.com/alexslemonade/scpcatools - 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: https://github.com/AlexsLemonade/scpcaTools/compare/v0.3.2...v0.4.0

- R
Published by jashapiro almost 2 years ago

https://github.com/alexslemonade/scpcatools - 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: https://github.com/AlexsLemonade/scpcaTools/compare/v0.3.1...v0.3.2

- R
Published by allyhawkins over 2 years ago

https://github.com/alexslemonade/scpcatools - 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: https://github.com/AlexsLemonade/scpcaTools/compare/v0.3.0...v0.3.1

- R
Published by allyhawkins over 2 years ago

https://github.com/alexslemonade/scpcatools - 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: https://github.com/AlexsLemonade/scpcaTools/compare/v0.2.3...v0.3.0

- R
Published by allyhawkins over 2 years ago

https://github.com/alexslemonade/scpcatools - 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 https://github.com/AlexsLemonade/scpcaTools/pull/184

Full Changelog: https://github.com/AlexsLemonade/scpcaTools/compare/v0.2.2...v0.2.3

- R
Published by allyhawkins almost 3 years ago

https://github.com/alexslemonade/scpcatools - 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: https://github.com/AlexsLemonade/scpcaTools/compare/v0.2.1...v0.2.2

- R
Published by sjspielman almost 3 years ago

https://github.com/alexslemonade/scpcatools - 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: https://github.com/AlexsLemonade/scpcaTools/compare/v0.2.0...v0.2.1

- R
Published by allyhawkins over 3 years ago

https://github.com/alexslemonade/scpcatools - 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 collapseintroncounts()

- R
Published by jashapiro over 3 years ago

https://github.com/alexslemonade/scpcatools - scpcaTools v0.1.9

What's Changed

  • Added Functions for conversion of SCE objects
    • to AnnData in https://github.com/AlexsLemonade/scpcaTools/pull/114
    • to Seurat in https://github.com/AlexsLemonade/scpcaTools/pull/116 & https://github.com/AlexsLemonade/scpcaTools/pull/123

  • Updated R tests for CI in https://github.com/AlexsLemonade/scpcaTools/pull/117

  • Use temp directory for intermediate files when rendering Notebooks in https://github.com/AlexsLemonade/scpcaTools/pull/125

Full Changelog: https://github.com/AlexsLemonade/scpcaTools/compare/v0.1.8...v0.1.9

- R
Published by jashapiro over 3 years ago

https://github.com/alexslemonade/scpcatools - scpcaTools v0.1.8

What's Changed

  • Updates to QC report to handle libraries with only one sample and cell hashing

Full Changelog: https://github.com/AlexsLemonade/scpcaTools/compare/v0.1.7...v0.1.8

- R
Published by allyhawkins about 4 years ago

https://github.com/alexslemonade/scpcatools - scpcaTools v0.1.7

What's Changed

  • Changes to QC report for libraries with multiplexing

Full Changelog: https://github.com/AlexsLemonade/scpcaTools/compare/v0.1.6...v0.1.7

- R
Published by allyhawkins about 4 years ago

https://github.com/alexslemonade/scpcatools - scpcaTools v0.1.6

What's Changed

  • Update to handle miQC filtering errors for certain rare model failures

Full Changelog: https://github.com/AlexsLemonade/scpcaTools/compare/v0.1.5...v0.1.6

- R
Published by jashapiro about 4 years ago

https://github.com/alexslemonade/scpcatools - scpcaTools v0.1.5

What's Changed

  • add_demux_vireo() function for integration of vireo genetic demux results
  • Made Seurat HTODemux() calls a bit more robust and fail more elegantly

Full Changelog: https://github.com/AlexsLemonade/scpcaTools/compare/v0.1.4...v0.1.5

- R
Published by jashapiro about 4 years ago

https://github.com/alexslemonade/scpcatools - scpcaTools v0.1.4

What's Changed

  • Handle failure for emptyDrops with a hard cutoff in filter_counts()
  • Adds function for Seurat demultiplexing results with add_demux_seurat()
    • Docker image now includes Seurat

Full Changelog: https://github.com/AlexsLemonade/scpcaTools/compare/v0.1.3...v0.1.4

- R
Published by jashapiro over 4 years ago

https://github.com/alexslemonade/scpcatools - scpcaTools v0.1.3

What's Changed

  • Rounding of alevin counts by default
  • Remove direct magrittr dependency
  • Add initial cellhash demux functions

Full Changelog: https://github.com/AlexsLemonade/scpcaTools/compare/v0.1.2...v0.1.3

- R
Published by jashapiro over 4 years ago

https://github.com/alexslemonade/scpcatools - scpcaTools v0.1.2

What's Changed

  • Minor QC report updates https://github.com/AlexsLemonade/scpcaTools/pull/70
  • Add test for filter_counts() & removed outdated feature stats when filtering https://github.com/AlexsLemonade/scpcaTools/pull/71
  • Update Bioconductor version to 3.14 for miQC 1.2.0 https://github.com/AlexsLemonade/scpcaTools/pull/72
  • Make emptyDropsCellRanger the default filtering method https://github.com/AlexsLemonade/scpcaTools/pull/76

Full Changelog: https://github.com/AlexsLemonade/scpcaTools/compare/v0.1.1...v0.1.2

- R
Published by jashapiro over 4 years ago

https://github.com/alexslemonade/scpcatools - scpcaTools v0.1.1

Changes in this version:

  • Added the function add_miQC() which runs miQC more robustly in the event of model failures
  • Added optional random seeds to filter_counts() and add_miQC()
  • Standardized format of axis legends in QC report

- R
Published by jashapiro over 4 years ago

https://github.com/alexslemonade/scpcatools - scpcaTools v0.1.0

Initial release of scpcaTools R package.

Includes functions for reading and manipulating single cell experiment results from various quantification pipelines, including generating a QC report.

- R
Published by jashapiro over 4 years ago