Leandro Hermida

R and radian paths per project folder/conda environment (i.e. make vscode-R design like vscode-python)

7

I'm new to VSCode (just moved from Atom because it's being retired), and I'm trying to understand how to set up the R extension to work seamlessly with conda environments...

Linting stops working or displaying in Atom with pyls > 0.31.2

35

After upgrading pyls on conda-forge from 0.31.2 -> 0.31.3 or 0.31.4 then ide-python suddenly stops showing any lint comments/warnings/errors. When I downgrade back to 0.31.2 then everything shows up again....

RFE/RFECV are not only feature selectors (SelectorMixin) but also classifiers/regressors (MetaEstimatorMixin), though ELI5 explain_weights doesn't support them as classifiers/regressors. The final fit of an RFE/RFECV object is a fitted estimator...

Add new paper to your rpy2 citations list

1

`rpy2` is an amazing library, I used it heavily in the following recent paper Hermida, L.C., Gertz, E.M. & Ruppin, E. Predicting cancer prognosis and drug response from the tumor...

Sample weights support in CoxnetSurvivalAnalysis and concordance_index_censored

1

`CoxnetSurvivalAnalysis` and `concordance_index_censored` (or model `score`) currently do not support sample weights and this would be very useful to have when calling `fit` and `score` using these methods. This is...

Pufferfish doesn't build within a conda environment (which has all the prerequisites) due to failed build of tslib from SeqLib

9

During `make` of pufferfish I'm getting the following error. You can see just above the error it does the presence and sanity checks for `zlib.h` and all good, so something...

It appears that the Pufferfish indexer supports using a gzipped FASTA reference file as input. Add description to help that it can do this.

gdcdata should not depend on internet connection when cache=TRUE and you have all the files in your local cache

1

The GDC data download function `gdcdata` should not depend on an internet connection when `cache=TRUE` and it finds that you have all the files it needs in your local cache.

filter syntax for GDC query API "IS MISSING" and "NOT MISSING" operators

6

Sorry if I missed it in the docs or somewhere, but what is the `filter` syntax for GQL "missing" and "not missing"?

`GenomicDataCommons` is a very powerful library and can query pretty much anything at the GDC, though many users prefer other libraries like e.g.,`TCGAbiolinks` because the `GenomicDataCommons` query results data structure,...