| title | description | category | subcategory | tags | |
|---|---|---|---|---|---|
Improvements for the analysis |
List of things to try. |
research |
orphans |
|
- Try out Alevin from Salmon for a more principled single-cell quantification (https://www.biorxiv.org/content/early/2018/06/01/335000)
- Add retained intron analysis with IRFinder to bcbio-nextgen
- See if adding support for grolar to convert pizzly output to something more parseable makes sense. It's an R script and hasn't really been worked on so might not be useable: https://github.com/MattBashton/grolar
- Add automatic loading/QC of bcbioSingleCell data from bcbio
- Convert bcbio-nextgen singlecell matrices to HDF5 format in bcbio
- Swap bcbioSingleCell to read the already-combined matrices for speed purposes
- Add bcbioRNASeq template to do DTU usage using DRIMseq (https://f1000research.com/articles/7-952/v1)
- Update installed genomes to use newest Ensembl build for RNA-seq for bcbio-supported genomes.