nmdp-bioinformatics/pipeline

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nmdp-bioinformatics/pipeline

nmdp-bioinformatics

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Consensus assembly and allele interpretation pipeline.

ngs

Next generation sequencing (NGS/HTS) tools.

py-ard

HLA ARD Reduction in Python

dash

Data Standards Hackathon for NGS based typing.

flow

Consensus assembly and variant calling workflow.

ImmunogeneticDataTools

Immunogenetic Data Tools related to HLA, GLStrings, Linkage Disequilibrium

igloader

HL7® FHIR® implementation guide uploader (from IGPack tarfile).

gfe-db

Graph database representing IPD-IMGT/HLA sequence data as GFE

grimm

GRIMM: Graph IMputation and Matching for HLA Genotypes

phycus

Service used for curation of Haplotype Frequency

act-service

Allele Calling Tool (ACT)

seq-ann

Python package for doing fast and accurate sequence annotation

multiple-allele-code

Services and libraries for handling multiple allele codes and IMGT/HLA nomenclature

flow-OptiType

Use nextflow to run BAM files through OptiType

BRIDGModel2Graph

BRIDG Model by version used to populate a Graph Database.

CIWD

CIWD data in computable form

service-epitope

T-cell epitope group matching service for HLA-DPB1 locus

imgt_biosqldb

The IMGT/HLA sequence data persisted in a BioSQL database

hml

Histoimmunogenetics Markup Language (HML).

imgt2aa

extract aligned amino acid sequences from IMGT/HLA

gfe-service

GFE Webservice: Provides REST endpoints to GFE related functions

hml-fhir-app

HML to FHIR Conversion Application

miring-validator

Semantic Validator for MIRING-compliant HML

flow-validation

Validation workflow.

py-graph-imputation

Graph Imputation

MiHAIP

genotype-list

Genotype List service, client library, and command line tools.

hla-reporting-ig

FHIR Implementation Guide for HLA reporting

service-feature

Enumerated sequence feature service.

gfe-docker-compose-app

GFE service and GFE Database Docker Compose

GFE

Gene Feature Enumeration for polymorphic genes

tarr2fhir

Convert tarr2fhir Sync4Genes - Versiti and GenDx

hml-validation-portal

Portal for HML validation

service-hml-fhir-converter

Mid level API to handle web-hmlFhirAngularClient

act-client

Python client for working with the ACT service

docker-validation

Docker container for the validation workflow.

service-hml

py-grimm

py-gfe

Python package for creating GFE notation from annotated sequences

cytoscape-donor-cluster

An implementation of the cytoscape.js network diagram applied to a donor search that was fitted with a SVM model

flow-GFE

Run fasta files through GFE with nextflow

nmdp-bioinformatics.github.io

Organization Website for NMDP Bioinformatics

ihiw-pedigree-sim

Simulation of ambiguous HLA typing data inherited within family pedigrees for 18th IHIW Project

flow-blast-hml

nextflow pipeline for extracting, blasting and validating all consensus sequences found in an HML file.

web-hml-fhir-converter

Client Application To Create HL7-Fhir messages with a base of HML