alanhoyle

Alan Hoyle's repositories

abra2

ABRA2

Language:JavaMIT020

alanhoyle

Config files for my GitHub profile.

030

autojump

A cd command that learns - easily navigate directories from the command line

Language:PythonNOASSERTION020

diceware

Passphrases to remember

Language:PythonGPL-3.0000

docker-images

Repository of Docker images created by Continuum Analytics

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duckyPad

Do-It-All Mechanical Macropad

Language:C++MIT020

duckyPad-macOS

A duckyPad config for macOS with SQL commands

MIT000

ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

Language:PerlApache-2.0000

FastQC

A quality control analysis tool for high throughput sequencing data

Language:JavaGPL-2.0020

fastvar

Some quick 'n dirty variant calling tools

Language:CMIT020

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

Language:C++MIT000

gaptools

dbGaP data validation tool repo

Language:ShellNOASSERTION000

gitignore

A collection of useful .gitignore templates

CC0-1.0000

good-enough-project

A good enough project template for writing reproducible code

Language:ShellMIT000

iTerm2

iTerm2 is a terminal emulator for Mac OS X that does amazing things.

Language:Objective-CGPL-2.0000

learngenomics.dev

A guided, intuitive introduction to genomics for software engineers. Curated by the community.

Language:JavaScriptNOASSERTION010

liquidprompt

A full-featured & carefully designed adaptive prompt for Bash & Zsh

Language:ShellAGPL-3.0000

LowCover

Report low coverage regions by e.g. gene given a coverage file and a targets definition file.

NOASSERTION000

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

Language:NextflowMIT000

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

Language:JavaScriptGPL-3.0000

nextflow

A DSL for data-driven computational pipelines

Apache-2.0000

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.

Language:JavaMIT020

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Language:C++GPL-3.0020

SMaSH

A tool for sample swap identification in high throughput sequencing studies

Language:Python020

teslausb

Steps and scripts for turning a Raspberry Pi into a useful USB drive for a Tesla

MIT000

test-datasets

Test data to be used for automated testing with the nf-core pipelines

MIT000

tools

Python package with helper tools for the nf-core community.

Language:PythonMIT010

vcf2maf

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

Language:PerlNOASSERTION020

vdjer

V'DJer - B Cell Receptor Repertoire Reconstruction from short read mRNA-Seq data

Language:CNOASSERTION010

vscode

Visual Studio Code

Language:TypeScriptMIT010