joyeuxnoel8

capnproto

Cap'n Proto serialization/RPC system - core tools and C++ library

pprof

pprof is a tool for visualization and analysis of profiling data

cereal

A C++11 library for serialization

GWA_tutorial

A comprehensive tutorial about GWAS and PRS

yas

Yet Another Serialization

cpp-serializers

Benchmark comparing various data serialization libraries (thrift, protobuf etc.) for C++

gggenomes

A grammar of graphics for comparative genomics

RagTag

Tools for fast and flexible genome assembly scaffolding and improvement

Liftoff

An accurate GFF3/GTF lift over pipeline

Blacklist

Application for making ENCODE Blacklists

ChromosomeMappings

This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

intervaltree

a minimal C++ interval tree implementation

regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.

susieR

R package for "sum of single effects" regression.

RaGOO

RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag

spoa

SIMD partial order alignment tool/library

paragraph

Graph realignment tools for structural variants

DALIGNER

Find all significant local alignments between reads

abPOA

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

mccortex

De novo genome assembly and multisample variant calling

dipcall

Reference-based variant calling pipeline for a pair of phased haplotype assemblies

ashr

An R package for adaptive shrinkage

RetroSeq

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.

ultra

Long-read splice alignment with high accuracy

dict

Dictionary with arbitrary keys and values for R

cosmo

Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.

jupyterext-text-shortcuts

A Jupyter Lab extension for keyboard text shortcuts

Iris

A module for improving the insertion sequences of structural variant calls

eagle

An R package for detecting Gene-by-Environment (GxE) interaction effects on the transcriptome using Allele Specific Expression quantified from RNA-seq

TopDownCrawl