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ag1000g-phase2-data-paper

Repo for building a data descriptor paper for the Ag1000G phase 2 resource.

agam-kilifi-report-2017

agam-report-base

anhima

Analyse genetic variation.

bioconda-recipes

Conda recipes for the bioconda channel.

chess

Code to evaluate a large PGN database

chessdata

R package containing data derived from *chess* repo. Includes functions to perform SQL queries and to put the data in readable form.

dotfiles

configuration files for tmux, vi, and bash

filesystem_spec

A specification that python filesystems should adhere to.

footballshiny

Simple scripts for scraping a football stats website and doing some basic R analysis. Results are available online.

futile.logger

A logging package in R similar to log4j

gaard_teaching

genomeplot

allows genome wide visualisations based on the bokeh library

geoparse

Python library to access Gene Expression Omnibus Database (GEO)

glickocalculator

A web based calculator for glicko ratings

hardingnj.github.io

Build a Jekyll blog in minutes, without touching the command line.

inda_h3bionet

Instructions and files for wk 2 of INDA h3bionet NGS course

ipython_docker

Dockerfile for running ipython in a docker container

llama

Inference code for LLaMA models

malariagen-data-python

A Python package providing convenience functions for accessing MalariaGEN public data.

mspy

Small Python library for parsing output from Hudson's MS

naf

Various NAF analyses

phasing

A few scripts/functions to help with the phasing analysis of ag-1000g

pychess

Supercedes hardingnj/chess. python >> perl

pyfaidx

Efficient pythonic random access to fasta subsequences

pyfurcation

Python functions to create haplotype bifurcation diagrams

pysamstats

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

rag1k

sample

Filter lines from standard input according to some probability, with a given delay, and for a certain duration.

scikit-allel

A Python package for exploring and analysing genetic variation data