Changelog

Source: NEWS.md

zellkonverter 1.6.0

  • Bioconductor 3.15, April 2022

zellkonverter 1.5.0 (2021-10-27)

  • Bioconductor 3.15 devel

zellkonverter 1.4.0 (2021-10-27)

  • Bioconductor 3.14, October 2021

zellkonverter 1.3.3 (2021-10-20)

  • Add progress messages to various functions
    • Can be controlled by function arguments or a global variable
  • Split konverter.R into two files (AnnData2SCE.R and SCE2AnnData.R)
  • Add arguments to control how slots are converted in AnnData2SCE() and SCE2AnnData() (Fixes #47)
    • Each slot can now be fully converted, skipped entirely or only selected items converted.
  • Add support for converting the raw slot to an altExp in AnnData2SCE() (Fixes #53, fixes #57)

zellkonverter 1.3.2 (2021-09-09)

  • Add recursive conversion of lists in AnnData2SCE()
  • Correctly handle DataFrame objects stored in adata.obsm
  • Remove pandas indexes from converted DataFrame objects
  • Add functions for validating SingleCellExperiment objects (for testing)
  • Add long tests for various public datasets

zellkonverter 1.3.1 (2021-06-22)

  • Fix bug in converting dgRMatrix sparse matrices (Fixes #55)

zellkonverter 1.3.0 (2021-05-20)

  • Bioconductor 3.14 devel

zellkonverter 1.2.0 (2021-05-20)

  • Bioconductor 3.13, May 2021

zellkonverter 1.2.1 (2021-06-22)

  • Fix bug in converting dgRMatrix sparse matrices (Fixes #55)

zellkonverter 1.1.11 (2021-05-19)

zellkonverter 1.1.10 (2021-05-18)

  • Update NEWS for release

zellkonverter 1.1.9 (2021-05-12)

zellkonverter 1.1.8 (2021-05-03)

zellkonverter 1.1.7 (2021-04-30)

  • Add compression argument to writeH5AD() (Fixes #49)
  • Update anndata Python dependencies, now using anndata v0.7.6

zellkonverter 1.1.6 (2021-04-27)

zellkonverter 1.1.5 (2021-03-05)

  • Better support for anndata SparseDataset arrays (PR #41, Fixes #37, Fixes #42)
  • More consistent conversion of metadata to uns in SCE2AnnData() (Fixes #40)
  • Add handling of list columns in colData and rowData in SCE2AnnData() (Fixes #26)
  • Export zellkonverterAnnDataEnv (Fixes #38)

zellkonverter 1.1.4 (2021-02-18)

zellkonverter 1.1.3 (2021-01-22)

zellkonverter 1.1.2 (2020-12-19)

  • Improved support for HDF5 backed conversion (PR #29, fixes #13)

zellkonverter 1.1.1 (2020-12-03)

  • Add example_anndata.h5ad file to inst/extdata/ and creation script to inst/scripts/
  • Improve conversion checks when converting .uns to metadata
  • Avoid converting obsp and varp to dense matrices

zellkonverter 1.1.0 (2020-10-28)

  • Bioconductor 3.13 devel

zellkonverter 1.0.0 (2020-10-28)

  • Bioconductor 3.12, October 2020

zellkonverter 1.0.3 (2021-03-08)

  • Avoid converting obsp and varp to dense matrices

zellkonverter 1.0.2 (2021-01-28)

  • Merge remaining commits for HDF5 conversion (fixes #33)

zellkonverter 1.0.1 (2021-01-26)

  • Improved support for HDF5 backed conversion (PR #29, fixes #13, fixes #33)

zellkonverter 0.99.7 (2020-10-16)

  • Update Python dependencies
    • numpy 1.18.5 -> 1.19.1
    • pandas 1.0.4 -> 1.1.2
    • scipy 1.4.1 -> 1.5.2
    • sqlite 3.30.1 -> 3.33.0

zellkonverter 0.99.6 (2020-10-12)

  • Document character to factor coercion in writeH5ad() (Fixes #6)
  • Add X_name argument to writeH5AD() (Fixes #23)

zellkonverter 0.99.5 (2020-09-28)

  • Tidy NEWS files for Bioconductor release

zellkonverter 0.99.4 (2020-08-28)

  • Bump anndata version to 0.7.4

zellkonverter 0.99.3 (2020-08-21)

  • Document the krumsiek11.h5ad file
  • Remove the internal keyword from the zellkonverter-package documentation

zellkonverter 0.99.2 (2020-08-21)

  • Update .gitignore

zellkonverter 0.99.1 (2020-07-15)

  • Fix SCE to AnnData map figure in PDF manual
  • Use expect_equal() instead of expect_identical() in writeH5AD() sparse matrices test
  • Edit package title and description

zellkonverter 0.99.0 (2020-07-10)

  • Initial Bioconductor submission

zellkonverter 0.0.0 (early development version)

zellkonverter 0.0.0.9017 (2020-07-10)

  • Add biocViews to DESCRIPTION
  • Edit package description
  • Tidy code
  • Replace 1:… with seq_len()

zellkonverter 0.0.0.9016 (2020-07-10)

  • Add check for scRNAseq in examples (Fixes #18)

zellkonverter 0.0.0.9015 (2020-07-02)

  • Skip AnnData matrices without a transposable R counterpart
  • Only replace skipped matrices when use_hdf5 = TRUE in readH5AD() (Fixes #12)
  • Additional tests for sparse matrices

zellkonverter 0.0.0.9014 (2020-06-30)

  • Allow assay skipping when converting from SingleCellExperiment to AnnData
  • Allow skipping of assays that aren’t numpy friendly in writeH5AD()
  • Wait for basilisk process shutdown to release .h5ad file
  • Updates to documentation and tests

zellkonverter 0.0.0.9013 (2020-06-25)

  • Improve conversion between SingleCellExperiment and AnnData (See #8)
    • Convert between metadata and uns (where objects are compatible)
    • Convert between rowPairs and varp
    • Convert between colPairs and obsp
    • Convert from varm to rowData (but not in reverse)
  • Add mapping table to docs

zellkonverter 0.0.0.9012 (2020-06-19)

  • Tidy documentation and code
  • Tidy vignette

zellkonverter 0.0.0.9011 (2020-06-18)

zellkonverter 0.0.0.9010 (2020-06-17)

  • Avoid checking column names for colData and rowData in SCE2AnnData()
  • Make sure that all matrices passes to {reticulate} are numpy friendly
  • Add more tests
  • Update vignette front matter

zellkonverter 0.0.0.9009 (2020-06-15)

  • Add vignette

zellkonverter 0.0.0.9008 (2020-06-12)

  • Add examples and improve documentation
  • Export .AnnDataDependencies for external use

zellkonverter 0.0.0.9007 (2020-06-11)

zellkonverter 0.0.0.9006 (2020-06-11)

zellkonverter 0.0.0.9005 (2020-06-09)

zellkonverter 0.0.0.9004 (2020-06-09)

  • Pin more AnnData dependencies (See #1)

zellkonverter 0.0.0.9003 (2020-06-08)

  • Add test .h5ad file
  • Add test for readH5AD()
  • Add package man page

zellkonverter 0.0.0.9002 (2020-06-08)

zellkonverter 0.0.0.9001 (2020-06-08)

  • Add {basilisk} infrastructure

zellkonverter 0.0.0.9000 (2020-06-08)

  • Set up package