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.