A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.

Repository for method to analyse the relationship between germline variants and somatic mutations and alternative splicing in breast cancer patients based on RNA-Seq data,

✂️ Trim sequencing adapters from NGS data automatically

nimble — execute lightweight, flexible alignments on arbitrary reference libraries

This repository contains the python package for Helical

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

LncDC: a machine-learning based tool for long non-coding RNA detection from RNA-Seq data

Code, documentation, and tutorial for the DGD model trained on bulk RNA-Seq data.

A Snakemake workflow to split, filter, normalize, integrate and select highly variable features of count matrices resulting from experiments with sequencing readout (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including diagnostic visualizations.

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

RNA sequencing analysis software

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

BRIE: Bayesian Regression for Isoform Estimate in Single Cells

Next-Gen Sequencing tools from the Horvath Lab

Deep Learning Based Tumor Type Classification Using Gene Expression Data

Package to study time series (or other series) multi-omics patterns of expresssion with replicates

all the scripts to reproduce the results in the splam paper

Customizable workflows based on snakemake and python for the analysis of NGS data