0.9.8

New functionality: minimal integration of SCENIC with scanpy (https://scanpy.readthedocs.io/en/latest/). The approach is fully explained in the Jupyter notebook: https://github.com/aertslab/pySCENIC/blob/master/notebooks/pySCENIC%20-%20Integration%20with%20scanpy.ipynb

0.9.7

• BugFix: Changed load_adjacencies to use fixed column types to avoid type errors (e.g. 'nan' as gene name in D. melanogaster incorrectly got interpreted as a floating point number).

0.9.6

• Added new Singularity file incorporating version tags.
• Small correction in documentation on Docker.
• BugFix: Incorrect warning message about number of genes being present in expression matrix when calculating recovery (based on #57).

0.9.5

Fixing versions for pandas and dask because github issues:

• #51
• #45

Fixed an issue where the regulon assignment matrix was not being added
to row attributes (loom output).

Changed lp.connect to read-only mode when importing expression matrix
from a loom file.

0.9.4

This release fixes an issue where the container images weren't properly updating after a new pySCENIC version was released.

0.9.3

• CLI: ability to choose algorithm used for gene regulatory network reconstruction.
• CLI: When loom file requested as output of aucell step, the regulon AUC values are appended as column attributes of a newly created loom file.

0.9.2

Minor updates for compatibility with SCope.

0.9.1

• CLI: BugFix for issue #39

0.9.0

• Command Line Interface (CLI): support for more file formats (e.g. loom and GMT format).
• Command Line Interface (CLI): new 'csv2loom' utility to convert an expression matrix as csv to loom.
• Differentiation of dependencies for CLI and Jupyter notebook usage: matplotlib dependency removed from the former.

0.8.16

Removed support for direct pruning of modules to regulons without the enriched motif table as intermediate.