knowledgebase

recipes that save time

View the Project on GitHub hbc/knowledgebase

  1. Try out Alevin from Salmon for a more principled single-cell quantification (https://www.biorxiv.org/content/early/2018/06/01/335000)
  2. Add retained intron analysis with IRFinder to bcbio-nextgen
  3. 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
  4. Add automatic loading/QC of bcbioSingleCell data from bcbio
  5. Convert bcbio-nextgen singlecell matrices to HDF5 format in bcbio
  6. Swap bcbioSingleCell to read the already-combined matrices for speed purposes
  7. Add bcbioRNASeq template to do DTU usage using DRIMseq (https://f1000research.com/articles/7-952/v1)
  8. Update installed genomes to use newest Ensembl build for RNA-seq for bcbio-supported genomes.