isoforms

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

A universal toolkit for upstream processing of long RNA reads

Single cell Nanopore sequencing data for Genotype and Phenotype

Discover differential transcript usage from polyA-captured single cell RNA-seq data

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

Simultaneous exploration of thousands of long-read transcriptomes by read-level indexing

Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data. See documentation at:

Python Client Library for the G2P Portal API

A GTF-native ORF annotation tool for transcriptomes

A Nextflow pipeline for end-to-end long-read proteogenomics analysis

interactive visualization of single-cell transcriptomes

Isoform function prediction and interpretation

A Snakemake pipeline developed to quantify isoforms expression levels in large RNA-seq datasets and find poly-A sites

pan-transcriptome splicing isoform analysis

👨🏻‍👩🏻‍👧🏻‍👦🏻Heritability + genetic correlation analyses for 🧠human brain isoform expression

Evidence-based refinement of Helixer deep-learning gene annotations. The prediction is the backbone; RNA-seq and protein evidence refine it only where they outscore it.

A webtool for visualizing alternative RNA isoforms across integrated long-read RNA-seq and pseudobulked single-cell short-read RNA-seq data.

Pipeline for the selection of canonical proteins for reference proteomes

Method to identify temporal and sex-specific alternative splicing from multi-omic data, specifically RNA-seq + (CUT&RUN or ChIP-seq).