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gffread -- GFF/GTF utility for filtering, converting, and extracting sequences from genome annotation files. Converts between GFF3 and GTF formats, extracts transcript (FASTA) and protein sequences fr

1 shared topic • 1 shared operation

IsoformSwitchAnalyzeR — R/Bioconductor package for detecting, annotating, and visualizing isoform switches with functional consequences from RNA-seq data. Integrates with Salmon, kallisto, StringTie,

1 shared topic • 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

1 shared topic • 1 shared operation

RSEM (RNA-Seq by Expectation-Maximization) — accurate gene and isoform quantification from RNA-seq data using EM algorithm with probabilistic multi-mapped read assignment. Supports STAR, Bowtie2, and

1 shared topic • 1 shared operation

salmon — Fast, bias-aware transcript quantification from RNA-seq data using selective alignment to the transcriptome. Supports bulk RNA-seq (mapping-based and alignment-based modes), single-cell RNA-s

1 shared topic • 1 shared operation