Daniel E Cook's repositories
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
sarek
Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing
redun
Yet another redundant workflow engine
deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
gist-alfred
An alfred workflow for accessing gists
cv
My Latex Resume template
danielecook.com
Source files for danielecook.com
python-cli-skeleton
Python argparse skeleton
seq-utilities-alfred
Alfred workflow with sequence utilities
andersenlab.github.io
Andersen Lab Website
nextflow-example
Example nextflow pipelines
BitVector
BitVector Implementation in Nim
tx_germline_snps
Running burden testing with SKAT on TRACERx data
bash-it
A community Bash framework.
packages
List of packages for Nimble
bamsurgeon-nextflow
:chart_with_upwards_trend: :wrench: A Nextflow wrapper around the BAMSurgeon program - https://github.com/adamewing/bamsurgeon
vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
codebox-alfred
An alfred workflow for accessing codebox snippets.
bam2fastq-nf
Convert a bam back to FASTQ