Trinity

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 • 3 shared operations

DRIMSeq is a Bioconductor R package for Differential Transcript Usage (DTU) analysis using a Dirichlet-multinomial distribution to model transcript-level count proportions. Tests whether relative tran

3 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

3 shared topics • 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,

2 shared topics • 2 shared operations

MAKER — portable genome annotation pipeline that integrates ab initio gene predictors (SNAP, Augustus, GeneMark), protein and EST evidence alignment, and repeat masking to produce GFF3 gene models wit

2 shared topics • 2 shared operations