CHANGELOG.md

Version 0.3.8

• Fixed bug when saving motif locations with network_from_motifs_fasta

Version 0.3.7

• Improved memory usage for network_from_motifs_fasta when a large number of sequences or TFs are used

Version 0.3.6

• Fix bug in saved location output

Version 0.3.5

• Fix bug when no regulators are found and saving locations is set.

Version 0.3.4

• Produce a filtered TF binding table when --save_filtered_location_data is set.

Version 0.3.3

• Correctly produced a TF binding table when --save_location_data is set.

Version 0.3.2

• Corrected a parsing error when reading CisBP PWM files

Version 0.3.1

• Added link_atac_bed_to_genes module to link specific peaks from a BED file to nearby genes

Version 0.3.0

• Finalized model for prior matrix thresholding

Version 0.2.3

• Added additional messaging and a --debug mode

Version 0.2.2

• Added additional messaging
• Restructured internal memory usage to be more efficient
• Added constraint lists for TFs and genes

Version 0.2.1

• Parallelized the final information matrix clustering and cutting
• Fixed a bug that included extra inappropriate edges in the final matrix in rare cases

Version 0.2.0

• Renamed to inferelator-prior
• Fully restructued and parallelized
• Implemented unit testing
• Changed edge selection logic to center around DBSCAN univariate clustering