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2022-01-19
LabKey
   Links and Resources

LabKey


Welcome to the RI-MUHC LabKey website.

For useful links and resources, click here.

For more information about LabKey, visit the LabKey Support Portal.




Links and Resources


RI-MUHC & McGill Campus

RI-MUHC Bioinformatics Platform

McGill Initiative in Computational Medicine (MiCM)

McGill University and Génome Québec Innovation Centre (MUGQIC)

Canadian Centre for Computational Genomics (C3G)

McGill HPC - McGill University's centre for High Performance Computing (HPC)

 

External links & resources

Bioinformatics

Bioinformatics.ca

GOBLET - the Global Organisation for Bioinformatics Learning, Education & Training

 

Genomics

Tools

IGV - Integrative Genomics Viewer

SSHFS (Windows, Linux) - Access remote file system by SSH

HTSeq - Analysing high-throughput sequencing data with Python

Illumina Open Source Software

vcfanno - Fast VCF annotator

cyvcf2 - Fast python parsing of VCF and BCF


Best practices & reference material

GATK Best Practices

NIH Genomic Data Commons (GDC)

´╗┐GEMSTAR, from The Transforming Genetic Medicine Initiative (TGMI)

Genome in a bottle (GIAB)

 

Variant databases

gnomAD and ExAC

ClinVar

 

Genome browsers

UCSC Genome Browser

Ensembl

Integrative Genomics Viewer (IGV)

 

Rare diseases

Online Mendelian Inheritance in Man (OMIM)

Orphanet

The Gene Curation Coalition

Genomics England PanelApp

ClinGen

 

Cancer

COSMIC

The Variant Interpretation for Cancer Consortium (VICC)

St. Jude PeCan

 

Ontologies

Human Phenotype Ontology (HPO)