Software Release and Tutorials

A fully-equipped, fast, memory-efficient pre-processor for ONT transcriptomic data

Cell type specific isoform estimator from bulk RNA-seq

Improving gene isoform quantification with miniQuant

Using long read RNAseq to catch the alternative Polyadenylation sites and monitor the lengthening or shortening trend of 3'UTRs

A pipeline for differential expression and differential alternative splicing analysis

PoGo is a proteogenomic tool which allows mapping of peptides identified through mass spectrometry to a reference genome through provided gene annotation.

TX2P - Transcript to protein

Assembler for multiple RNA-seq samples

Refinement tool for transcript isoform identification using long reads.

FusionInspector code

ChimPipe: Accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

"Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.

A tool for processing Split-seq reads to extract, correct, and tag barcodes, with statistical reports and visualizations.

tools for working with genome variation graphs

Differential quantification of alternative splicing events on spliced pangenome graphs

GFHunter is a long read sequence transcriptome alignment-based fusion genes detection tool

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing

DeepSAP repository for documentation and supplemental data

Tool for IDentification and Enumeration of Spliced and Unspliced Read Fragments

single cell Cross- Annotation and Multimodal Estimation on Lineage trajectory

trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.

Comprehensive and scalable differential splicing analyses

Nextflow pipeline for performing parallel alternative splicing analysis using rMATS and Whippet and then overlapping the results.

splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq