danielecook

Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

gist-alfred

An alfred workflow for accessing gists

seq-collection

gg

Github Gists from the command line. On MAC OSX, it (will be) an Alfred Workflow!

tut

A collection of CSV/TSV Utilities

python-cli-skeleton

Python argparse skeleton

codebox-alfred

An alfred workflow for accessing codebox snippets.

still

Unit testing for spreadsheets

TIL-Tool

A tool for creating and indexing Today I Learned (TILs)

danielecook.github.io

seq-utilities-alfred

Alfred workflow with sequence utilities

nucleus

Python and C++ code for reading and writing genomics data.

vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

andersenlab.github.io

Andersen Lab Website

bam2fastq-nf

Convert a bam back to FASTQ

bamsurgeon-nextflow

:chart_with_upwards_trend: :wrench: A Nextflow wrapper around the BAMSurgeon program - https://github.com/adamewing/bamsurgeon

bash-it

A community Bash framework.

BitVector

BitVector Implementation in Nim

city-area

cv

My Latex Resume template

danielecook

danielecook.com

Source files for danielecook.com

DEC-Notes

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

nextflow-example

Example nextflow pipelines

packages

List of packages for Nimble

redun

Yet another redundant workflow engine

sarek

Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing

TIL

tx_germline_snps

Running burden testing with SKAT on TRACERx data