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bioinformatics

braker

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

callpeak

call peaks from DNase-seq data

chorus2

A pipeline to select oligonucleotides for fluorescence in situ hybridization (Oligo-FISH).

chorus_perl

A perl implement of Chorus idea. Checkout https://github.com/forrestzhang/Chorus

compile-vim

convert-vcf-to-hapmap

csvkit

A suite of utilities for converting to and working with CSV, the king of tabular file formats.

deeptools

Tools to process and analyze deep sequencing data.

diane

Dashboard for the Inference and Analysis of Networks from Expression data

ensembl-compara

The Ensembl Compara Perl API and SQL schema

entropy

maize_v4_te_annotation

scripts and intermediate files used to annotate TEs in Jiao et al.

minineedle

Needleman-Wunsch and Smith-Waterman algorithms in python

nerdtree-cheat-sheet

networkx

Official NetworkX source code repository.

paf2delta

convert paf to delta format

pycoverage

parallel version of coverageBed from bedtools

pylcs

super fast cpp implementation of longest common subsequence/substring

quota-alignment

Guided synteny alignment between duplicated genomes (within specified quota constraint)

shortcutkeys

tmux.conf

current tmux setting

tulip

TULIP - The Uncorrected Long read Itegration Pipeline

vim-python-ide

Python development config with asynchronous Vim Plugins

vr-codebase

The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute