reg-gen
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CostaLab
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Hello. I have histone data in addition to ATACseq, and I was interested in running the footprinting analysis on the histone data as well as on the classical ATACseq. Unfortunately...
Hi, this is a nice piece of software. I was wondering if it would be possible to let the user control where the input data was coming from, instead of...
In some (still rare) cases, RGT (or one of its dependencies) cannot be installed successfully, or it's too hard to make it work. We should aim to provide one package...
* the organism should be added * evaluate all needed options * gene names should be sanitised before joining
Related to #117, but more general and thus deserving of its own issue. AnnotationSet `fix_gene_names` by default converts gene names to upper case. This is unnecessary when proper organism resolution...
We currently have a `toString` method, a `str` special method, and a `repr` method. They must be reworked to be efficient and consistent. `toString` could become a "private" method used...
The current test does not use inputs, and thus it doesn't test as much as it could do. We need to replace it (or better, just add another one).
Currently a GRS has a list containing GenomicRegions. However, many times we already have subsequences - the most common example is a chromosome. If I'm trying to intersect MPBS regions...
Hi @fabio-t , I needed a bioconda recipe for "RGT", so I created one, https://anaconda.org/bioconda/rgt. The download of the database is not part of the recipe due to its size,...
