Bambu

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

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

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

2 shared topics • 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

2 shared topics • 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

2 shared topics • 1 shared operation