- Fix bugs in RNAseq
- Add function to set up library
- re-structure templates
- Add text with best practices
- Reproducibility:
- test data for RNAseq, singlecell, CHIPseq
- Base project:
- Guidelines to create repo easily
- Example Rmd with headers and aesthetics
- RNASEQ
- Use provenance for FA in DE report
- Support multiple comparisons
- New templates:
- methylation - draft
- singcell cell QC and Inegration - stable
- scQC shiny app - stable
- chipseq QC and Diffbind - beta
- COSMX - draft
- fix duplicated gene names
- Add combatseq
- Add draft templates for TEAseq, COSMX
- Adapt templates to nf-core rnaseq
- Fix when sample start by number
- Fix when rRNA rate is missing
- Add by sample plots in QC
- Add function to check nfcore samplesheet
- Add PCA with variance analysis
- Minor details fixed in QC RNAseq report
- Correct metric for rRNA and tRNA
- Add page to github
- Make CHECK to pass
- Add vignette