jmschrei/tfmodisco-lite

Issues

• `MergeMotifsAcrossRuns.ipynb` should account for indexes with respect to `--window`

  #48 opened 4 months ago by KnightAsterial
  0

• How are high absolute attribution scores defined?

  #47 opened 4 months ago by FelixWaern
  1

• --verbose is still rather taciturn

  #45 opened 5 months ago by mmtrebuchet
  1

• `modisco meme` command does not return trimmed motifs and no negative patterns but only positive ones

  #44 opened 8 months ago by ThorbenMaa
  3

• Center peak regions at summit in `modisco seqlet-bed`

  #43 opened 9 months ago by austintwang
  1

• `example_idx` doesnt trace back to original contribution scores

  #39 opened 9 months ago by mlweilert
  1

• Reset seqlet coordinates with respect to "--window"

  #20 opened a year ago by jvierstra
  1

• Need to raise an error if the attr or ohe files don't end in `.npz` or `.npy`

  #38 opened 10 months ago by jmschrei
  0

• Errors from MEME text parser leads to pandas.errors.EmptyDataError: No columns to parse from file

  #37 opened 10 months ago by anupamajha1
  1

• Add Unit tests

  #34 opened a year ago by bytewife
  0

• Add command to extract seqlets info in BED and FASTA format

  #24 opened a year ago by jmschrei
  0

• Add negative pattern implementation for `meme` subcommand

  #30 opened a year ago by bytewife
  0

• Add example folder containing notebooks

  #22 opened a year ago by jmschrei
  0

• Add MEME output from modisco motifs

  #23 opened a year ago by jmschrei
  0

• motifs.html report can be confusing

  #26 opened a year ago by janewangsmile
  0

• version for RNA sequence

  #25 opened a year ago by janewangsmile
  0

• Create reports without meme database

  #5 opened a year ago by mmtrebuchet
  2

• Access motifs

  #21 opened a year ago by samuel-g-bates
  0

• Add Linting Github Action

  #19 opened a year ago by bytewife
  1

• Request of the example data

  #7 opened a year ago by Gavin-Lijy
  3

• Running tfmodisco-lite for multiple tasks?

  #13 opened a year ago by ioansarr
  4

• Doesn't work for the the sequences in variable lengths

  #14 opened a year ago by ruizhideng
  2

• Could not construct partition: Cannot accept NaN weights.

  #12 opened a year ago by avantikalal
  1

• tabs vs spaces

  #9 opened a year ago by hopdebee
  1

• Motifs missing when input sequence less than 400 bp

  #11 opened a year ago by ziwei-75
  1

• Does tfmodisco-lite work with sequences that contain N?

  #10 opened a year ago by coffeebond
  2

• No motifs found

  #8 opened a year ago by SalimMegat
  1

• Attribution scores vs importance scores

  #1 opened 2 years ago by due23
  2

• Arial Rounded not available on my system

  #4 opened a year ago by mmtrebuchet
  1

• Matrix format of pfms in motif pfms directory

  #3 opened 2 years ago by due23
  3

• Generating report: pandas.errors.EmptyDataError: No columns to parse from file

  #2 opened 2 years ago by due23
  1