Release Notes

0.12.1 | 2022-11-21

  • Add support for running arboreto_with_multiprocessing.py with spawn instead of fork as multiprocessing method.Pool
  • Use ravel instead of flatten to avoid unnecessary memory copy in aucell
  • Update Docker image file and add separated Docker file for pySCENIC with scanpy.

0.12.0 | 2022-08-16

  • Only databases in Feather v2 format are supported now (ctxcore >= 0.2), which allow uses recent versions of pyarrow (>=8.0.0) instead of very old ones (<0.17). Databases in the new format can be downloaded from https://resources.aertslab.org/cistarget/databases/ and end with *.genes_vs_motifs.rankings.feather or *.genes_vs_tracks.rankings.feather.
  • Support clustered motif databases.
  • Use custom multiprocessing instead of dask, by default.
  • Docker image uses python 3.10 and contains only needed pySCENIC dependencies for CLI usage.
  • Remove unneeded scripts and notebooks for unused/deprecated database formats.

0.11.2 | 2021-05-07

  • Split some core cisTarget functions out into a separate repository, ctxcore. This is now a required package for pySCENIC.

0.11.1 | 2021-02-11

  • Fix bug in motif url construction (#275)
  • Fix for export2loom with sparse dataframe (#278)
  • Fix sklearn t-SNE import (#285)
  • Updates to Docker image (expose port 8787 for Dask dashboard)

0.11.0 | 2021-02-10

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

0.10.4 | 2020-11-24

  • Included new CLI option to add correlation information to the GRN adjacencies file. This can be called with pyscenic add_cor.

0.10.3 | 2020-07-15

  • Integrate arboreto multiprocessing script into pySCENIC CLI
  • Skip modules with zero db overlap in cisTarget step
  • Additional error message if regulons file is empty
  • Additional error if there is a mismatch between the genes present in the GRN and the expression matrix
  • Fixed bug in motif url construction when running without pruning

0.10.2 | 2020-06-05

  • Bugfix for CLI grn step

0.10.1 | 2020-05-17

  • CLI: file compression (optionally) enabled for intermediate files for the major steps: grn (adjacencies matrix), ctx (regulons), and aucell (auc matrix). Compression is used when the file name argument has a .gz ending.

0.10.3 | 2020-07-15

  • Integrate arboreto multiprocessing script into pySCENIC CLI
  • Skip modules with zero db overlap in cisTarget step
  • Additional error message if regulons file is empty
  • Additional error if there is a mismatch between the genes present in the GRN and the expression matrix
  • Fixed bug in motif url construciton when running without pruning

0.10.2 | 2020-06-05

  • Bugfix for CLI grn step

0.10.1 | 2020-05-17

  • CLI: file compression (optionally) enabled for intermediate files for the major steps: grn (adjacencies matrix), ctx (regulons), and aucell (auc matrix). Compression is used when the file name argument has a .gz ending.

0.10.0 | 2020-02-27

  • Added a helper script arboreto_with_multiprocessing.py that runs the Arboreto GRN algorithms (GRNBoost2, GENIE3) without Dask for compatibility.
  • Ability to set a fixed seed in both the AUCell step and in the calculation of regulon thresholds (CLI parameter --seed; aucell function parameter seed).
  • (since 0.9.18) In the modules_from_adjacencies function, the default value of rho_mask_dropouts is changed to False. This now matches the behavior of the R version of SCENIC. The cli version has an additional option to turn dropout masking back on (--mask_dropouts).