Jacki Buros Novik
Jacki Buros Novik
I often create `Patient` objects where a required attribute (e.g. `os`) is also in the clinical data for that subject. I tend to name these fields using self-explanatory but short...
Often, `tqdm` prints progress bars on multiple lines and it can be annoying to scroll through. This can happen in a trivial fashion, where there is occasionally a single line...
Per PR #199, which fixed a bug in py2 due to unicode `id` variables. Would be good practice to add a unit test for this scenario.
@jburos commented on [Tue Apr 25 2017](https://github.com/hammerlab/msk-bms-lung/issues/77) This came up recently (e.g. in PR hammerlab/msk-bms-lung#75 & issue hammerlab/msk-bms-lung#42). Since this is also now relevant for an RCC analysis I thought...
Currently benefit is coded as a binary status - True/False. It would be nice to support ordered categories, such as `{0: "No response", 1: "Partial Response", 2: "Complete Response"}`. In...
Would be useful to keep track of `batch` identifiers so we can estimate batch effects as part of standard protocol.
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...
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...
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...