Daniel E Cook's repositories
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
gist-alfred
An alfred workflow for accessing gists
python-cli-skeleton
Python argparse skeleton
codebox-alfred
An alfred workflow for accessing codebox snippets.
seq-utilities-alfred
Alfred workflow with sequence utilities
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
danielecook.com
Source files for danielecook.com
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
tx_germline_snps
Running burden testing with SKAT on TRACERx data