Katarzyna Sikora

- [x] deprecate mode Gruen scRNAseq - [ ] remove mode Gruen functionality entirely - [ ] make ``--fromBAM`` work the same way between workflows - [ ] rename ``--skipVelocyto``...

- [ ] check which organisms need update in e.g. ensemble version - [ ] add GRCz11 - [ ] check if software can be bumped in env yamls -...

HiC workflow qc plots

1

- [ ] add HiC QC plot - [ ] add HiC correlate plot - given sample sheet, run HiC correlate for replicates belonging to one condition - [ ]...

a/o SNARE-seq2

* Fixes #836

Matrix rendering much faster when NOT using the shiny wrapper

2

Hi, we've noticed the matrix rendering (say matrix(rnorm(200000), 10000)) is very slow using morpheus(x) in shiny, but rendering from a text file opened via what looks like a morpheus iframe...

add support for custom model formula to mRNAseq and other workflows

2

- [x] mRNAseq DESeq2 - [ ] mRNAseq sleuth - [ ] noncoding RNAseq - [ ] WGBS - [ ] ATAC-seq - [ ] ChIP-seq