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bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bowtie

Cookbook for installing Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. http://bowtie-bio.sourceforge.net/

bwa-meth

align BS-Seq reads and extract methylation without intermediate temp files

celery

Distributed Task Queue (development branch)

celery-tutorial

chef-continuum-anaconda

Chef cookbook for Continuum Analytic's Anaconda: "completely free Python distribution for large-scale data processing, predictive analytics, and scientific computing"

cutadapt

cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.

django-rest-tutorial

ensembl

The Ensembl Core Perl API and SQL schema

ensembl-hive

EnsEMBL Hive - a system for creating and running pipelines on a distributed compute resource

ensembl-hive-sge

ensembl-hive

ensembl-pipeline

Job management for the Ensembl Genebuild pipeline

ensembl-production

Ensembl Production code

ensembl-rest

Language agnostic RESTful data access to Ensembl data over HTTP

ensembl-webcode

The code to run an Ensembl website

epiexplorer

EpiExplorer is a web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborous preprocessing.

fastapi-utils

Reusable utilities for FastAPI

globomantics

h5serv

Reference service implementation of the HDF5 REST API

nodejs_noodling

Noodling with Node.js

pact_playing

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

pluralsight-working-with-components-in-react18

pluralsight-working-with-components-in-react18

ps-react-fundamentals

public-plugins

Plugins for an Ensembl website

pyinstaller-template

Simple example of pyinstaller usage including package directory an exe build

pysam

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

qualimap

Evaluating next generation sequencing alignment data

samtools

Cookbook for installing Samtools, a suite of programs for interacting with high-throughput sequencing data.

sanic-swagger-ui

Swagger UI blueprint for sanic