kundajelab/chrombpnet
Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
Jupyter NotebookMIT
Issues
- 2
installation error on Mac M1
#195 opened by ratheraarif - 2
- 1
Job killed during ChromBPNet training
#192 opened by eunksung - 2
Input for training cell type-specific models
#194 opened by marzamKI - 1
Error with convert_html_to_pdf
#196 opened by viramalingam - 1
Input file shifts inconsistent
#198 opened by AlGaydosik - 4
Cannot access example files - 403 Forbidden
#199 opened by terencewtli - 1
problem in 'motif hit calling'
#193 opened by GGboy-Zzz - 1
Error while training ChromBPNet with pre-trained bias model on example dataset
#186 opened by sadhanagaddam3 - 3
- 1
For CUT&RUN do you recommend ChromBPNet or BPNet?
#185 opened by gdolsten - 1
Rev comp to augment sequences
#187 opened by saninta0212 - 1
Confusion matrix
#190 opened by arodel21 - 1
Lower precision for inference
#191 opened by kairukuma - 5
- 1
- 4
Training chromBPNet takes too much time
#161 opened by lzj1769 - 2
Obtaining BAM file with removed TN5-bias
#182 opened by arodel21 - 2
Difference between counts and profile
#178 opened by arodel21 - 1
Nit: Small inconsistency on "Generate contribution score bigwigs" wiki page for names of output files
#181 opened by KnightAsterial - 1
chrombpnet_deepshap command not found
#183 opened by saninta0212 - 2
- 0
- 7
provenance of tn5 motif meme data?
#177 opened by mkarikom - 9
Model performance: Pearson correlation score
#173 opened by arodel21 - 5
Input file shifts inconsistent
#174 opened by monikaheinzl - 11
- 6
- 7
Question on pred_bw
#149 opened by ZixiaoWang17 - 12
missing chromosomes when using reads_to_bigwig.py
#172 opened by cmlakhan - 1
TFmodisco lite doesn't seem to run
#175 opened by rb56 - 6
footprint bw track
#168 opened by YichaoOU - 1
- 1
- 3
Predicting bias
#167 opened by arodel21 - 4
- 1
contribs_bw slow?
#166 opened by YichaoOU - 1
- 17
- 1
Using chrombpnet for STARR-Seq data
#158 opened by otastet - 5
Generating contribution score bigwig file
#162 opened by PetHabib - 8
TypeError: get_regions() missing 1 required positional argument: 'regions_used'
#154 opened by MZZheng - 11
`qc` broken b.c. it expects auxiliary folder to simultaneously exist and not exist
#160 opened by bytewife - 1
Error generating bigwig files in contribution score
#164 opened by rb56 - 0
Thresholds for bias model pearsonr performance
#159 opened by rb56 - 5
Error while training the bias model
#155 opened by rb56 - 1
- 17
Error while shifting ATAC peaks
#153 opened by arodel21 - 1
- 1
Question about outputs of Variant effect prediction
#152 opened by jasondanic