Software dev - kundajelab/chrombpnet GitHub Wiki

Preprocessing wrapper to start from bam and auto-generate non-peaks and peaks - https://github.com/kundajelab/chrombpnet/issues/89
Multi-task training - https://github.com/kundajelab/chrombpnet/issues/108
Add support for bed3 format while making prediction bigwigs - https://github.com/kundajelab/chrombpnet/issues/118. To add support for the following (1) Merge the input bed file (2) Make overlapping windows for the merged bed file using bedtools makewindows. (window size 1000bp and overlapping by at least 250bp) (3) Create summits centered on the center of the windows to make predictions.
Remove dependency on deepdish and use h5py loading directly. Revert to updating numpy.
Check if deeplift at lower-precision is faster - https://github.com/kundajelab/chrombpnet/issues/191
Continuing pipeline from set point - https://github.com/kundajelab/chrombpnet/issues/207