kundajelab chrombpnet issues

kundajelab / chrombpnet

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

https://github.com/kundajelab/chrombpnet/wiki

MIT License

124 stars 34 forks source link

issues

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how to extract contribution scores using genomic positions

#213 Brawni opened 1 week ago
0
how to pass mean contribution scores to TFmodisco

#212 Brawni opened 3 weeks ago
0
Malformed BED entry error during chrombpnet training

#211 cahn20 closed 1 month ago
0
chrombpnet prep nonpeaks does not complete

#210 Brawni opened 1 month ago
2
Plugging peak calls from ArchR

#209 Brawni opened 1 month ago
0
Scipy nanmean issue in predict.py for chrombpnet docker

#208 pl92297 opened 2 months ago
0
Continuing pipeline from set point

#207 BartTheeuwes closed 2 months ago
1
chrombpnet for Mac M2

#206 wgao688 closed 2 months ago
1
Error Encountered During Bias Model Training for ATAC-seq Data

#205 ys3508 opened 2 months ago
9
Does ChromBPNet normalize the input data at any point?

#204 idf-io closed 3 months ago
2
Seeking Advice on Comparing ChromBPNet Predictions Across Models

#203 XuanrZhang closed 2 months ago
1
Generating nonpeaks data

#202 saninta0212 opened 4 months ago
0
Nanmean is deprecated, imported, unused, and never tested

#201 thomas-reimonn opened 4 months ago
1
chromBPNet training questions

#200 kaillahs closed 2 months ago
29
Cannot access example files - 403 Forbidden

#199 terencewtli closed 4 months ago
4
Input file shifts inconsistent

#198 AlGaydosik closed 2 months ago
1
Input file shifts inconsistent (Arabidopsis)

#197 hermandebeukelaer opened 5 months ago
2
Error with convert_html_to_pdf

#196 viramalingam closed 2 months ago
1
installation error on Mac M1

#195 ratheraarif closed 2 months ago
2
Input for training cell type-specific models

#194 marzamKI closed 4 months ago
2
problem in 'motif hit calling'

#193 GGboy-Zzz closed 5 months ago
1
Job killed during ChromBPNet training

#192 eunksung closed 2 months ago
1
Lower precision for inference

#191 kairukuma closed 5 months ago
1
Confusion matrix

#190 arodel21 closed 5 months ago
1
data_unstranded.bw is sparse and has a different range

#189 ArnovanHilten closed 6 months ago
1
Invalid interval bounds when predicting bigwigs with ground truth

#188 hdbeukel closed 5 months ago
5
Rev comp to augment sequences

#187 saninta0212 closed 5 months ago
1
Error while training ChromBPNet with pre-trained bias model on example dataset

#186 sadhanagaddam3 closed 5 months ago
1
For CUT&RUN do you recommend ChromBPNet or BPNet?

#185 gdolsten closed 5 months ago
1
Using uncorrected chrombpnet model for generation of prediction bigwigs

#184 Gechyb closed 5 months ago
3
chrombpnet_deepshap command not found

#183 saninta0212 closed 8 months ago
1
Obtaining BAM file with removed TN5-bias

#182 arodel21 closed 8 months ago
2
Nit: Small inconsistency on "Generate contribution score bigwigs" wiki page for names of output files

#181 KnightAsterial closed 8 months ago
1
Discrepancy between coords self.coords between peak and nonpeak sequences

#180 zrcjessica opened 9 months ago
2
Choice of NEG_TO_POS_RATIO_TRAIN in preparing background region

#179 saninta0212 opened 10 months ago
0
Difference between counts and profile

#178 arodel21 closed 8 months ago
2
provenance of tn5 motif meme data?

#177 mkarikom closed 10 months ago
7
Input file shifts inconsistent with bowtie2 and MACS3

#176 jingliulj closed 10 months ago
11
TFmodisco lite doesn't seem to run

#175 rb56 closed 10 months ago
1
Input file shifts inconsistent

#174 monikaheinzl closed 10 months ago
5
Model performance: Pearson correlation score

#173 arodel21 closed 10 months ago
9
missing chromosomes when using reads_to_bigwig.py

#172 cmlakhan closed 10 months ago
12
aggressive filtering when generating peaks for bias training

#171 cmlakhan closed 10 months ago
1
possible discrepancy in count filtering for bias model?

#170 cmlakhan closed 10 months ago
1
Error while shifting ATAC reads; similar to issue #153

#169 viramalingam closed 10 months ago
6
footprint bw track

#168 YichaoOU closed 10 months ago
6
Predicting bias

#167 arodel21 closed 11 months ago
3
contribs_bw slow?

#166 YichaoOU closed 11 months ago
1
Typo in argument parsing within `preprocessing/reads_to_bigwig.py`

#165 KnightAsterial closed 11 months ago
1
Error generating bigwig files in contribution score

#164 rb56 closed 11 months ago
1