Sean Ephraim's repositories
bin4matics
A bin/ -like directory filled with CLI executables for bioinformatics and informatics usage
convert_MacArthur_ClinVar_TSV_to_VCF
Download the latest release of the MacArthur Lab's version of ClinVar in TSV format and convert it to a VCF file
GenomeSnax
An easy way to query your Genome Trax MySQL database by gene, region, position, or specific variant.
get_ESP6500SI_AC_AN_AF_tags
Modify the original ESP6500SI VCF files to contain AC, AN, and AF tags like ExAC and 1000 Genomes
hg19_gene_and_mitochondrial_regions
All gene symbols and their respective hg19 chromosomal regions
auto_retry_gitlab_ci
Auto-retry failing jobs on GitLab CI
carton_caps_api_docs
Documentation for the Carton Caps API
convert_1000Gp3_VCFs
Combine, normalize and format all 1KG phase 3 VCFs to include AC, AN, and AF for each super-population
convert_ClinVar_XML_to_VCF
Convert a ClinVar XML file to a VCF file
convert_dbNSFP_to_BCF
Combine all variant annotation files from dbNSFP into a single BCF file
devcontainers
.devcontainer templates
ecard-sushi
Sushi project for HTML5/Javascript e-card
get_ExAC_AC_AN_AF_tags
Modify the original ExAC VCF file to contain only AC, AN, AF tags for all populations
git_templates
Git templates directory including sample hooks
hgvs_variant_converter
Convert HGVS names from NC to NM (and vice versa) and infer NP protein changes
iterm2-material-design
A theme / color scheme for iTerm2 based on Google's Material Design Color Palette
manage_duplicates_in_VCF
Manage records in a VCF that have a matching CHROM, POS, REF, and ALT
sephraim.github.io
Build a Jekyll blog in minutes, without touching the command line.