Transcriptional Regulatory Inference Analysis from Gene Expression (TRIAGE)

Flimma is a federated privacy-aware version of state-of-the-art differential expression analysis method limma voom.

Visualizing transcript structure and annotation using ggplot2

RAPToR (Real Age Prediction from Transcriptome staging on Reference) is a tool to accurately predict individual samples' developmental age from their gene expression profiles.

A Comprehensive and Robust Framework for Identifying Promoters in Multiple Species

RNAchallenge dataset for the classification of protein-coding and non-coding RNAs

Building Gene Regulatory Networks in scRNA-seq data, https://doi.org/10.1186/s13059-023-02897-x

Deep-learning Augmented RNA-seq analysis of Transcript Splicing

The ubiquitously expressed genes in human (Housekeeping Genes)

scover

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

A Shiny-based framework to analyze and visualize interactively genomic data

An R interface to the MEME Suite

🎯 ChIP peak Annotation, Comparison and Visualization

Transcript Distance Calculations

deep learning-inspired explainable sequence model for transcription initiation

IsoVis enables fast and informative visualization of isoform structures and expression levels.

SUPPA: Fast quantification of splicing and differential splicing

A computational workflow for exitron splicing identification

Snakemake-based computational workflow for neoantigen prediction from diverse sources

IRIS: Isoform peptides from RNA splicing for Immunotherapy target Screening

Keep Me Around: Intron Retention Detection