pre-release-v1.1

What's Changed

• gc-matching and preprocess by @panushri25 in #1
• fixed consistency in gc_matched_negatives by @panushri25 in #3
• Preprocessing by @panushri25 in #2
• Variant effect prediction by @panushri25 in #4
• changed output_dir to output_prefix to align with script by @kmualim in #5
• Fixed bug with merged bam file directory in data download step of tut… by @amanpatel101 in #7
• fix typos in documentation by @kmualim in #8
• Fixes to docker image and tutorial by @amanpatel101 in #9
• seed set properly to ensure reproducibility by @panushri25 in #19
• adding pseudocount to prevent div by 0 error by @annashcherbina in #13
• added commands to stop any shell script on error and return fail code by @annashcherbina in #12
• Fixed misspelling of "median_norm_jsd" by @amanpatel101 in #21
• Fixed pandas errors - added changes this time lol by @amanpatel101 in #15
• invivo footprinting changes to fit to the new format by @panushri25 in #22
• Changing marginal footprinting operate on the test chromosomes, not a single hardcoded one by @amanpatel101 in #20
• fix typo by @ziwei-75 in #23
• Fast genomewide GC binning by @austintwang in #11
• Remove "import keras" from predict_to_bigwig.py by @amanpatel101 in #24
• Updated version of Modisco in requirements.txt by @amanpatel101 in #25
• removing unused/empty chrombpnet_with_bias_bigwig.py file by @annashcherbina in #35
• added model arg to fetch_snp_predictions function by @annashcherbina in #34
• typo fix by @annashcherbina in #32
• typo fix by @annashcherbina in #33
• changed --output_dir to --output_png as the code expects a path to an… by @annashcherbina in #36
• option to provide ylim for marging footprint plotting by @annashcherbina in #27
• Faster genomewide gc counting by @suragnair in #30
• Maintain consistency with get_genomewide_gc_bins.py by @panushri25 in #38
• make num_shuffles a param and replace hard coded values of 20 by @annashcherbina in #39
• Improving modisco tomtom html documentation by @annashcherbina in #56

New Contributors

• @panushri25 made their first contribution in #1
• @kmualim made their first contribution in #5
• @amanpatel101 made their first contribution in #7
• @ziwei-75 made their first contribution in #23
• @suragnair made their first contribution in #30

Full Changelog: https://github.com/kundajelab/chrombpnet/commits/v1.1