Anthony Tan comments

Results 15 comments of


                                            Anthony Tan

run.neighborhoods.py Dimension Mismatch

We've revamped the codebase. Please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main and reopen your issue if it still exists

Use with single-cell ATAC-Seq?

We've revamped the codebase. Please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main and reopen your issue if it still exists We have a section dedicated to scATAC-seq in the ReadTheDocs

Is it possible to include HiC data for GRCh38?

We've revamped the codebase. Please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main and reopen your issue if it still exists average HiC is available in the linked ReadTheDocs in the detailed methods section

How to get .KRobserved files from .hic file type?

We've revamped the codebase. Please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main and reopen your issue if it still exists

juicebox_dump.py

We've revamped the codebase. Please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main and reopen your issue if it still exists

Running predict.py: VCobserved doesn't exist, but the program keeps looking for it

We've revamped the codebase. Please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main and reopen your issue if it still exists

'neighborhoods.py' (line 448) ~> pandas dataframe size mismatch on assertion in function 'count_single_feature_for_bed'

We've revamped the codebase. Please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main and reopen your issue if it still exists

KeyError(key) in run.neighborhoods.py

We've revamped the codebase. Please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main and reopen your issue if it still exists

Index Error during Step 2

We've revamped the codebase. Please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main and reopen your issue if it still exists

Install QC

are you referring to the QC plots generated from the example run? If so, I wouldn't really compare to the example as it's only based on chromosome 22.