Skip to content

0.11.0
Compare
Choose a tag to compare
@cflerin cflerin released this 10 Feb 13:20
· 91 commits to master since this release
0.11.0
001c9ad

Major features:

  • Updated Arboreto release (GRN inference step) includes:

    • Support for sparse matrices (using the --sparse flag in pyscenic grn, or passing a sparse matrix to grnboost2/genie3).
    • Fixes to avoid dask metadata mismatch error

  • Updated cisTarget:

    • Fix for metadata mismatch in ctx prune2df step
    • Support for databases Apache Parquet format
    • Faster loading from feather databases
    • Bugfix: loading genes from a database (previously missing the last gene name in the database)

  • Support for Anndata input and output

  • Package updates:

    • Upgrade to newer pandas version
    • Upgrade to newer numba version
    • Upgrade to newer versions of dask, distributed

  • Input checks and more descriptive error messages.

    • Check that regulons loaded are not empty.

  • Bugfixes:

    • In the regulons output from the cisTarget step, the gene weights were incorrectly assigned to their respective target genes (PR #254).
    • Motif url construction fixed when running ctx without pruning
    • Compression of intermediate files in the CLI steps
    • Handle loom files with non-standard gene/cell attribute names
    • Reformat the genesig gmt input/output
    • Fix AUCell output to loom with non-standard loom attributes
Assets 2
Loading