PCAWG Pipelines

Use when working with VAST-TOOLS for alternative splicing analysis in RNA-seq data. Routes to references and scripts for VASTDB setup, splicing event quantification (PSI/PIR), differential splicing wi

3 shared topics • 2 shared operations

FLAMES — Full-Length Analysis of Mutations and Splicing for bulk and single-cell long-read RNA-seq data. R/Bioconductor pipeline for barcode demultiplexing, isoform discovery, transcript quantificatio

2 shared topics • 3 shared operations

Graph-based alignment of reads to a population of genomes using hierarchical indexing — successor to TopHat and HISAT for RNA-seq alignment.

2 shared topics • 3 shared operations

Use when working with nf-core/rnafusion — a Nextflow pipeline for RNA fusion gene detection and quantification. Detects fusion transcripts from RNA-seq data using up to six callers (STAR-Fusion, Arrib

3 shared topics • 1 shared operation

Poetry is the Python dependency management and packaging tool for creating reproducible projects with pyproject.toml and poetry.lock. Use this skill for dependency resolution, virtual environment isol

2 shared topics • 2 shared operations