Comments (1)
j-andrews7
commented on August 21, 2024
I now expect to use mygene's query command for this, which should simplify things.
Best idea would likely be to query expression file and add columns for Ensembl, Entrez, and gene symbol IDs, then query the motif file as it's iterated through and find if any of those three IDs for the motif match and filter it that way. Will actually likely simplify things and take care of some of the issues with expression stuff in general.
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Related Issues (20)
- Print command to header.
- Handle multiple motifs for same TF. HOT 1
- Allow iterative or parallel processing for ChIP-seq data. HOT 1
- Motif clustering as a potential feature.
- control and documented runs HOT 2
- Other motif scanning/comparison tools.
- motifs.py bugs, tests & refactors HOT 3
- tf_expression.py bugs, tests & refactors
- thresholds.py bugs, tests, and refactors
- activity.py bugs, tests & refactors HOT 2
- get_motifs length all not individual TF HOT 2
- tf_expression: bed file format HOT 1
- variant code duplication HOT 2
- gene_expression.py bugs, tests & refactors
- motifs.py output order right investigation HOT 8
- 'join' used as method name in motif.py HOT 2
- Many motif databases provide PFMs rather than count matrices
- summarize.py bugs, tests, & refactors
- Position of variant within motif.
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