v0.1.7

Full Changelog: v0.1.6...v0.1.7

v0.1.6

Fixes issue #150 and handles filtering of regions for contribution bigwig building correctly. The user no longer needs to pre-filter regions as mentioned in the wiki for generating contribution scores.

Full Changelog: v0.1.5...v0.1.6

v0.1.5

Full Changelog: v0.1.4...v0.1.5

v0.1.4

• (MAJOR) Bug in chrombpnet modisco_motifs command. seqlets was limited to 50000. If users wanted to change it to 1 million this did not happen.
• Filter peaks at edges for pred_bw command and bias pipleline. So bias evaluation now done on these filtered peaks.
• Preprocessing deafulted to use unix sort. Provided option to switch to bedtools sort.
• Provided option to use filter chromosomes option in preprocessing.

Full Changelog: v0.1.3...v0.1.4

v0.1.3

What's Changed

• fix: correct misspelling resonse->response in output files by @riyavsinha in #107
• Migrate from tensorflow-gpu to tensorflow by @austintwang in #105
• Temporary patch to fix deepish incompatibility with numpy (will replace deepdish in future versions)
• Added ISMB talk to documentation

Full Changelog: v0.1.2...v0.1.3

v0.1.2

What's Changed

• Consolidate docker layers by @annashch-insitro in #85
• fix: modify preprocessing to filter reads from chroms not in ref fasta by @riyavsinha in #87
• Added scripts to compress deepshaps, float16 on shaps and int8 on the raw
• modisco-lite version upgrade

New Contributors

• @annashch-insitro made their first contribution in #85
• @riyavsinha made their first contribution in #87

Full Changelog: v0.1.1...v0.1.2

v0.1.1

What's Changed

• Made marginal foot-printing check stringent by checking for < 0.003 across all motifs
• Fixed Chrombpnet pipeline issue in generating pdf/html files for DNase
• Moved to using bedtools sort instead of unix sort
• Set counts loss weight to 1 for both chrombpnet and bias model when reads are low - should now accomodate low read data as well
• fixed typo bug in chrombpnet modisco run
• Testing low read run by @panushri25 in #84

Full Changelog: v0.1.0...v0.1.1

v0.1.0

Initial pypi release

v1.3-pre-release

moving to branch