GTFtools

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

3 shared topics • 1 shared operation

miRDeep2 — de novo microRNA (miRNA) discovery and quantification from small RNA-seq data. Identifies known and novel miRNAs by mapping collapsed reads to the genome, scoring hairpin structures, and co

3 shared topics

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

2 shared topics • 1 shared operation

scikit-allel — Python package for exploratory analysis of large-scale genetic variation data. Provides data structures for genotypes, haplotypes, and allele counts (GenotypeArray, HaplotypeArray, Alle

2 shared topics • 1 shared operation

STAR-Fusion — detects candidate fusion transcripts from RNA-seq data using STAR alignments and the FusionInspector validation framework. Integrates with CTAT genome resource libraries for comprehensiv

2 shared topics • 1 shared operation