cohorts
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hammerlab
Utilities for analyzing mutations and neoepitopes in patient cohorts
This is an enhancement that would be nice to have, but is not technically required at this point. This is in part to address the question (_Does cohorts make VCFs...
We're currently frozen on `varcode` and `isovar`, and also have version limits on `topiary` and `mhctools`. We need to fix `cohorts` to work on the latest versions of all these...
Taking (now closed) PR #116 & turning it into a feature request for discussion. ## Goal Rather than printing `missense_snv_col` in plots, print `Missense SNV Count / MB` or `Missense...
Feature request from @jburos
I get the following error when trying to load variant effects from the TCGA-BLCA cohort E.g, if I were to use `missense_snv_count` instead of `snv_count` in [this notebook](https://github.com/jburos/tcga-blca/blob/master/Part%20II%20-%20Creating%20a%20cohort%20from%20clinical%20%26%20SNV%20data%20using%20python2.ipynb) This looks...
Once that's done, `Patient` no longer needs to point to `Cohort`.
At https://github.com/hammerlab/cohorts/blob/master/cohorts/load.py#L613-L619 - Is there a reason which catch this `IOError` and treat it the same as not having provided a VCF path? Any objections to removing that catch and...
E.g. do not merge all `VariantCollection`s for a `Patient` automatically if from different tumor samples
Seems very easy to accidentally forget the following lines at the beginning of functions: ``` filter_fn = first_not_none_param([filter_fn, cohort.filter_fn], no_filter) normalized_per_mb = first_not_none_param([normalized_per_mb, cohort.normalized_per_mb], False) ``` ...and thereby not use...