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CHANGELOG.md

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Changelog

Version - 1.5

  • Fixed issue #150, regions_used not found while generating bigwigs from impotance h5s

Version - 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.

Version - 1.3 - Inworks - 2022-12-11

  • Changed pipelines to use modisco-lite, old modisco will soon be removed
  • Added automatic shift scripts to repo and integrated with the pipeline
  • modisco now outputs both html and pdf. pdf can be shared with anyone.
  • Use ATAC, DNASE not ATAC_PE, DNASE_SE anymore.
  • Simplyfing workflows to include only two main workflows, chrombpnet_train_tf_model, chrombpnet_train_bias_model
  • Restructuring README, moving tutorial to additional documentation and introducing FAQ, and only two pipelines (chrombpnet_train_tf_model, chrombpnet_train_bias_model)

[Unreleased] - 2022-02-28

  • Typo fix - (PR#31-36)
  • We can now specify ylimit in marginal footprinting plots (PR#27)
  • PR#30 merged to do fast genome wide gc binning and bug fix to ensure case-sensitve GC calculation. Adds a unit test to make checks.

[Unreleased] - 2022-02-11

  • Updated modisco version - (PR#25)

[Unreleased] - 2022-02-07

  • Typo fix - (PR#23-24)

[Unreleased] - 2022-01-31

  • Marginal footprinting no longer hardcoded to take only chr1, it now inputs the fold json. (PR#20)
  • Invivo footprinting is made compatible with the new input repo changes. (PR#22)
  • Pandas read bugs fixed for gc-matching scripts. (PR#15)
  • Tutorial now exits when one part of the pipeline breaks instead of proceeding further. (PR#18)
  • Added the fast binning scripts at src/helpers/make_gc_matched_negatives/get_genomewide_gc_buckets (PR#11)
  • Added pseudocount in metrics.py (PR#13) - needs further review.

[Unreleased] - 2022-01-24

  • Seed setting fixed for training. Seed was set improperly - preventing shuffling for every epoch. (PR#19)
  • return coordinates while training for debugging - returns status of the point such as revcomp,peak/nonpeak,coordinates etc

[Unreleased] - 2022-01-15

  • In step6_train_chrombpnet_model changed the file saving name bug
  • Changed scripts in src/evaluatuion/make_bigwigs/ to be compatible with new dir structure

[Unreleased] - 2022-01-13

  • Added a note in README that users can continue to use the pre-trained bias model from chrombpnet-lite repo, if thats what they have been using till now
  • Changed the default modisco crop setting in tutorial from 1000 to 500
  • Fixed a bug in src/evaluation/modisco/run_modisco.py in directory creation