A standalone and free application to explore genetics variations from VCF file

A collection of Galaxy-related training material

A pipeline for differential expression and differential alternative splicing analysis

Bioinformatics analysis scripts, workflows, general code examples

Code and annotations for the Tabula Muris single-cell transcriptomic dataset.

ChIP-seq peak-calling, QC and differential analysis pipeline.

ATAC-seq peak-calling and QC analysis pipeline

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Please consider using/contributing to https://github.com/nf-core/sarek

'ggplot2' Based Publication Ready Plots

TransDecoder source

NaS is a hybrid approach developped to take advantage of data generated using MinION device. We combine Illumina and Oxford Nanopore technologies to produce NaS (Nanopore Synthetic-long) reads of u…

RNA-seq aligner

A tool for assessing the library saturation without alignment

R/qtl: A QTL mapping environment

Java utilities for Bioinformatics

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

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

MERLIN performs common pedigree analyses. Input files describe relationships between individuals in your dataset, store marker genotypes, disease status and quantitative traits and provide informat…

Simple variant caller - Please update to the latest version !