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NMDP/Be The Match Bioinformatics Research

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Repositories

aws_expense_estimator: A perl script intended to predict month-end AWS computing costs by extrapolating from expenses-to-date. Note that the farther along in the month you are, the more accurate this will be.
cibmtr-smart-ansible-public: null
cookiecutter-pypackage: Cookiecutter template for a Python package.
cytoscape-donor-cluster: An implementation of the cytoscape.js network diagram applied to a donor search that was fitted with a SVM model
dash: Data Standards Hackathon for NGS based typing.
data-table-examples-hover-sort: example code to do the data tables hover and collapse features using qtip2
Deb_Lecture: SQL code development lecture
docker-ars: Docker container for the ARS service.
docker-blast-hml: null
docker-flow: Docker container for flow.
docker-flow-nmdp: Docker container for flow with NMDP specific implementation details.
docker-validation: Docker container for the validation workflow.
fhir-connectathon: This is a public repository for HL7 FHIR connectathon-related work.
fhir-submission: null
flow: Consensus assembly and variant calling workflow.
flow-blast-hml: nextflow pipeline for extracting, blasting and validating all consensus sequences found in an HML file.
flow-GFE: Run fasta files through GFE with nextflow
flow-OptiType: Use nextflow to run BAM files through OptiType
flow-validation: Validation workflow.
genotype-list: Genotype List service, client library, and command line tools.
gfe-db: Graph database representing IPD-IMGT/HLA sequence data as GFE
grimm: GRIMM: Graph IMputation and Matching for HLA Genotypes
gtr-tools: null
hapi-fhir: HAPI FHIR - Java API for HL7 FHIR Clients and Servers
haplotype-frequency-service: Service that accepts Haplotype/Genotype Data
hgtr: null
HiddenMarkovLecture: Accompanying lab code for Hu's hidden markov lecture
hml: Histoimmunogenetics Markup Language (HML).
hml-fhir: null
hml-fhir-app: HML to FHIR Conversion Application
hml-fhir-conversion: null
hml-fhir-mongo: null
hml-to-fhir: Converts HML to HL7 FHIR
HSA: null
imgt2aa: extract aligned amino acid sequences from IMGT/HLA
imgt_biosqldb: The IMGT/HLA sequence data persisted in a BioSQL database
ImmunogeneticDataTools: Immunogenetic Data Tools related to HLA, GLStrings, Linkage Disequilibrium
kafka-consumer: null
kafka-producer: null
liftoverGL: null
mcmc-lab: null
MiHAIP: null
miring-validator: Semantic Validator for MIRING-compliant HML
multiple-allele-code: Services and libraries for handling multiple allele codes and IMGT/HLA nomenclature
netMHC-spark: netMHC Apache Spark CLI
ngs: Next generation sequencing (NGS/HTS) tools.
nmdp-spark-hml: Apache Spark support for HML
pipeline: Consensus assembly and allele interpretation pipeline.
process-kafka-fhir-hml-conversion-consumer: null
process-kafka-fhir-submission-consumer: null
process-kafka-hml-fhir-conversion-consumer: null
process-kafka-hml-fhir-parent: null
pwm: pwm
pyARD: HLA ARS reduction in python
pyGFE: Python package for creating GFE notation from annotated sequences
pyglstring: Sanity check for GL String
pyHML: Python package for working with HML
Search_Productivity_Publication: Analysis Code for the Search Productivity Analysis
SeqAnn: Python package for doing fast and accurate sequence annotation
service-act: Allele Calling Tool (ACT)
service-ars: ARS reduction service
service-common: Services common libraries.
service-epitope: T-cell epitope group matching service for HLA-DPB1 locus
service-feature: Enumerated sequence feature service.
service-fhir-submission: null
service-gfe-submission: Service for getting a GFE from raw sequence data.
service-haplotype-frequency-creation: Service used for creation of Haplotype Frequency
service-haplotype-frequency-curation: Service used for curation of Haplotype Frequency
service-hml: HML service.
service-hml-fhir-converter: Mid level API to handle web-hmlFhirAngularClient
service-hml-fhir-converter-api: null
service-hml-fhir-converter-models: null
service-hml-fhir-converter-parent: null
service-kafka-producer-model: null
service-parent: Services parent pom.
service-population: Service to register and lookup population
util-swagger-codegen-models: null
web-hml-fhir-conversion-dashboard: null
web-hml-fhir-converter: Client Application To Create HL7-Fhir messages with a base of HML

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.