Releases: OpenOmics/leafworker
v0.2.0
leafworker (v0.2.0)
Feature: Add in a step to run IsoformSwitchAnalyzeR with or without covariates to find differential isoform usage/switching.
- Adding new rule to generate leafviz Rdata file.
- Adding new docker image with IsoformSwitchAnalyzeR dependencies.
- Adding docker image with ISA dependencies.
- Adding bam2fq step for running salmon, step to build salmon index, salmon-quant step, step to create a raw and normalized counts matrix, and a step to run ISA
- Adding quantify transcripts option to conditionally run IsoformSwitchAnalyzeR
Big fixes:
- Unset any R-related ENV vars related to system-level and user-level R package installations
- Updating renaming of col names for ISA sample sheet
Full Changelog: v0.1.0...v0.2.0
v0.1.0
leafworker (v0.1.0)
This is the first public release of leafworker. This release marks a significant milestone in the development of leafworker.
About
Leafworker was designed to simplify the process of running leafcutter on hundreds or thousands of samples. It was designed to be highly scalable and reproducible. This release implements all the upstream data-processing steps for running leafcutter, and it performs leafcutter's differential splicing analysis. If you use leafworker, please don't forget to cite leafcutter. This pipeline is a wrapper around the leafcutter, a tool for the analysis of RNA-seq data to identify and quantify alternative splicing events.
Full Changelog: https://github.com/OpenOmics/leafworker/commits/v0.1.0