Jay Hesselberth

https://rnabioco.github.io/djvdj/articles/clustering.html#cdr3-motifs so they come out `1,2,3...` instead of `1,10,11...`

move external data sets to ExperimentHub

3

CRAN / Bioconductor won't allow downloading of external data; it won't pass their checks. We can't use `download.file` anywhere. Need to: 1. Generate a smaller data set (a sample of...

ROC analysis of CITE-seq / AVID-seq reagents

2

Thoughts on [ROC analysis](https://en.wikipedia.org/wiki/Receiver_operating_characteristic) of protein-DNA tags as classifiers. The question is how well a given reagent performs as a classifer relative to gene expression classifications (i.e., assuming these are...

Identify useful data sets

4

- Probably don't want to bundle AVID-seq data until it's published. - LIBRA-seq? - Other large TCR or BCR sequencing data sets?

Have been thinking lately about doing a deep mutational scan on the MD4 BCR. Would be different way to see if changes in affinity can be accurately measured by AVID-seq.

Implement dark mode

6

Copies relevant, recent work from rstudio/bslib kudos to @gadenbuie related to #1696

Run a sitrep at the end of each build?

3

Seems useful to debug problems early.

https://pkgdown.r-lib.org/authors.html#citation

This fixes a known gcc parser bug that croaks on `= 6.

I get errors during compilation with `gcc` < 6.0 (`gcc` >=6.0 and `clang++` are fine). ``` C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"c:/R/include" -DNDEBUG -I../inst/include -I"c:/RLibrary/Rcpp/include" -I"c:/RLibrary/BH/include" -I"c:/RLibrary/dplyr/include" -I"d:/Comp In file included from ../inst/include/valr.h:6:0,...