IsoformSwitchAnalyzeR

GTFtools — Python command-line toolkit for parsing, analyzing, and converting GTF/GFF gene annotation files. Extracts gene, transcript, and exon features; computes transcript lengths, exon counts, and

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 • 1 shared operation

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 • 2 shared operations

Leafcutter — annotation-free RNA splicing quantification from short-read RNA-seq data. Detects differential intron usage, alternative splicing events, outlier splicing (LeafcutterMD), and splicing QTL

2 shared topics • 2 shared operations

Trinity — de novo transcriptome assembler for RNA-seq data. Reconstructs full-length transcript isoforms without a reference genome using three sequential modules: Inchworm (greedy k-mer assembly), Ch

2 shared topics • 2 shared operations