kundajelab/chrombpnet

Issues

• how to pass mean contribution scores to TFmodisco

  #212 opened 2 months ago by Brawni
  0

• Malformed BED entry error during chrombpnet training

  #211 opened 2 months ago by cahn20
  0

• chrombpnet prep nonpeaks does not complete

  #210 opened 3 months ago by Brawni
  2

• Plugging peak calls from ArchR

  #209 opened 3 months ago by Brawni
  0

• Input file shifts inconsistent

  #198 opened 3 months ago by AlGaydosik
  1

• chrombpnet for Mac M2

  #206 opened 3 months ago by wgao688
  1

• Seeking Advice on Comparing ChromBPNet Predictions Across Models

  #203 opened 3 months ago by XuanrZhang
  1

• Continuing pipeline from set point

  #207 opened 3 months ago by BartTheeuwes
  1

• chromBPNet training questions

  #200 opened 3 months ago by kaillahs
  29

• Error with convert_html_to_pdf

  #196 opened 3 months ago by viramalingam
  1

• installation error on Mac M1

  #195 opened 3 months ago by ratheraarif
  2

• Job killed during ChromBPNet training

  #192 opened 3 months ago by eunksung
  1

• Scipy nanmean issue in predict.py for chrombpnet docker

  #208 opened 3 months ago by pl92297
  0

• Error Encountered During Bias Model Training for ATAC-seq Data

  #205 opened 4 months ago by ys3508
  9

• Does ChromBPNet normalize the input data at any point?

  #204 opened 4 months ago by idf-io
  2

• Nanmean is deprecated, imported, unused, and never tested

  #201 opened 6 months ago by thomas-reimonn
  1

• Generating nonpeaks data

  #202 opened 5 months ago by saninta0212
  0

• Input file shifts inconsistent (Arabidopsis)

  #197 opened 6 months ago by hermandebeukelaer
  2

• Input for training cell type-specific models

  #194 opened 6 months ago by marzamKI
  2

• Cannot access example files - 403 Forbidden

  #199 opened 6 months ago by terencewtli
  4

• problem in 'motif hit calling'

  #193 opened 6 months ago by GGboy-Zzz
  1

• Error while training ChromBPNet with pre-trained bias model on example dataset

  #186 opened 7 months ago by sadhanagaddam3
  1

• Using uncorrected chrombpnet model for generation of prediction bigwigs

  #184 opened 7 months ago by Gechyb
  3

• For CUT&RUN do you recommend ChromBPNet or BPNet?

  #185 opened 7 months ago by gdolsten
  1

• Rev comp to augment sequences

  #187 opened 7 months ago by saninta0212
  1

• Confusion matrix

  #190 opened 7 months ago by arodel21
  1

• Lower precision for inference

  #191 opened 7 months ago by kairukuma
  1

• Invalid interval bounds when predicting bigwigs with ground truth

  #188 opened 7 months ago by hdbeukel
  5

• data_unstranded.bw is sparse and has a different range

  #189 opened 7 months ago by ArnovanHilten
  1

• Obtaining BAM file with removed TN5-bias

  #182 opened 9 months ago by arodel21
  2

• Difference between counts and profile

  #178 opened 9 months ago by arodel21
  2

• Nit: Small inconsistency on "Generate contribution score bigwigs" wiki page for names of output files

  #181 opened 9 months ago by KnightAsterial
  1

• chrombpnet_deepshap command not found

  #183 opened 9 months ago by saninta0212
  1

• Discrepancy between coords self.coords between peak and nonpeak sequences

  #180 opened 10 months ago by zrcjessica
  2

• Choice of NEG_TO_POS_RATIO_TRAIN in preparing background region

  #179 opened a year ago by saninta0212
  0

• provenance of tn5 motif meme data?

  #177 opened a year ago by mkarikom
  7

• Model performance: Pearson correlation score

  #173 opened a year ago by arodel21
  9

• Input file shifts inconsistent

  #174 opened a year ago by monikaheinzl
  5

• Input file shifts inconsistent with bowtie2 and MACS3

  #176 opened a year ago by jingliulj
  11

• Error while shifting ATAC reads; similar to issue #153

  #169 opened a year ago by viramalingam
  6

• missing chromosomes when using reads_to_bigwig.py

  #172 opened a year ago by cmlakhan
  12

• TFmodisco lite doesn't seem to run

  #175 opened a year ago by rb56
  1

• footprint bw track

  #168 opened a year ago by YichaoOU
  6

• possible discrepancy in count filtering for bias model?

  #170 opened a year ago by cmlakhan
  1

• aggressive filtering when generating peaks for bias training

  #171 opened a year ago by cmlakhan
  1

• Predicting bias

  #167 opened a year ago by arodel21
  3

• contribs_bw slow?

  #166 opened a year ago by YichaoOU
  1

• Typo in argument parsing within `preprocessing/reads_to_bigwig.py`

  #165 opened a year ago by KnightAsterial
  1

• Generating contribution score bigwig file

  #162 opened a year ago by PetHabib
  5

• Error generating bigwig files in contribution score

  #164 opened a year ago by rb56
  1