Michael Steinbaugh

S4 methods

2

Hi @jennybc, would you be up for merging a pull request that documents how to access S4 methods? If so, I can work on adding that to the markdown. Best,...

Bioconda recipe

18

Would it be possible to publish this on Bioconda in addition to PyPi? I'm happy to help write and submit a recipe.

New `rd_section_minidesc` error with roxygen2 7.2.1

3

With the roxygen2 7.2.1 update, I'm now seeing this error in one of my packages, and I'm having trouble locating the source: ``` Error in rd_section_minidesc(name = object_name(block$object), desc =...

Bad binding access

20

I'm seeing this error pop up inside of RStudio when attempting to call `lobstr::obj_size()`. I'm working on attempting to make a reprex. Just wanted to see if this is a...

Install issue of rgl v0.105.22 on macOS in Homebrew

15

Hi, I'm having trouble getting rgl to install on one of my Macs running macOS 10.15.7. I tested this on another computer running Big Sur 11.2.2 and rgl installs sucessfully....

@naumenko-sa We should update the r-bcbiornaseq environment to the 0.4 release series. I'm working on pushing the r-bcbiornaseq 0.4.1 recipe update to bioconda, but 0.4.0 is currently available for testing...

`degCovariates`: breaking change in dplyr filter code

6

Hi @lpantano , hope you're doing well! I'm seeing an error in `bcbioRNASeq::plotPCACovariates()` due to a breaking change in `DEGreport::degCovariates()`. Here's the traceback: ```r library(bcbioRNASeq) data(bcb) plotPCACovariates(bcb) > packageVersion("DEGreport") [1]...

Feature request: bioconda recipe

5

Hi @ryanlayer, I'm interested in writing a bioconda recipe for giggle. Would you be up for helping me with this? Best, Mike

pancan_pcawg_2020 and pan_origimed_2020

4

Hi Waldron Lab, I'm working on migrating my cBioPortal workflow code to use cBioPortalData, and the package is really excellent. Great work. One thing that I've noticed is that `pancan_pcawg_2020`...

`theme_bw()` is hard-coded in some plots

2

Hi, I noticed that `theme_bw()` is called inside `plotEnrichment()`, which makes it more difficult to customize. Would it be possible to remove this? See also: https://github.com/ctlab/fgsea/search?q=theme_bw&unscoped_q=theme_bw The current ggplot2 recommendation...