🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Fast and accurate gene fusion detection from RNA-Seq data

Fast, efficient RNA-Seq metrics for quality control and process optimization

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

✂️ Deep learning-based splice site predictor that improves spliced alignments

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

Big data Regression for predicting DNase I hypersensitivity

GCEN: an easy-to-use toolkit for Gene Co-Expression Network analysis and lncRNAs annotation

Fast in-silico normalization algorithm for NGS data

Mapping-free software for fishing relevant reads in an RNA-Seq sample

A tool for de novo clustering of long transcriptomic reads

A sensitive and fast tool for circular RNA detection from RNA-Seq data

K-mer indexing and querying in RNA-Seq data

rnabridge-align is an efficient tool to bridge paired-end RNA-seq reads

Assembler for multiple RNA-seq samples

bamcc — split SAM/BAM files into connected components

An assembler for circular RNAs