Pinned Repositories
civic-client
Web client for CIViC: Clinical Interpretations of Variants in Cancer
civic-v2
CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer
DeepSVR
GenVisR
Genome data visualizations
pVAC-Seq
DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
pVACtools
regtools
Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
rnabio.org
website for the rnaseq course
rnaseq_tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
VAtools
A set of tools to annotate VCF files with expression and readcount data
The Griffith Lab's Repositories
griffithlab/pVAC-Seq
DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
griffithlab/DeepSVR
griffithlab/rnaseq_tutorial_wiki
The wiki repo, with pull request enabled, for the rnaseq_tutorial
griffithlab/convert_zero_one_based
Python CLI to convert between zero and one based genomic coordinate systems
griffithlab/gen-viz-lectures
lectures for genviz.org workshop kept separate for performance
griffithlab/BGA-interface-projects
Monorepo for user-interface projects of the Bioinformatics and Genome Analytics group at MGI
griffithlab/bioinformatic-workflows
CWL workflows for bioinformatic analysis
griffithlab/civic-api-docs
Beautiful static documentation for your API
griffithlab/civic-panel
Tools for selecting targets for and designing panel for various assays
griffithlab/civic2clinvar
extraction of CIViC variants into the clinvar submission format
griffithlab/CRC_biomarkers
Repo for analysis of CRC biomarkers from stool samples
griffithlab/neoag_protocol
Protocol for end-to-end neoantigen analysis and vaccine design for a single patient
griffithlab/gnomad_annotation
Python package to add gnomAD allele frequencies to MGI annotated files
griffithlab/brain-tumor-heterogeneity
Code for figures
griffithlab/cancer-hotspots
Predicting neoantigens from cancer hotspots
griffithlab/CIViC_PM
Open-sourced Precision Medicine Pathway using CIViC Annotations
griffithlab/command_line_bootcamp
:computer: command-line bootcamp adventure in your browser
griffithlab/docker-civicpy
Docker containerization of the CIViCpy package - https://github.com/griffithlab/civicpy - civicpy.org
griffithlab/epics
The project management repo of the Griffith Lab
griffithlab/genvisr.org
Companion website for the GenVisR library
griffithlab/jekyll_template
Work to enhance existing jekyll sites
griffithlab/MCL_project
Scripts used for the MCL data pipeline
griffithlab/open-data-registry
A registry of publicly available datasets on AWS
griffithlab/precision_medicine_KISC
This is the precision medicine KISC site/lab manual
griffithlab/pvac-seq-client
browser client for the pVAC-Seq project
griffithlab/saturation-mutagenesis-viz
Shiny app for visualizing functional data from saturation mutagenesis assays (TP53, SMAD4, etc.)
griffithlab/saturation-mutagenesis-website
Companion website to the saturation mutagenesis toolkit
griffithlab/sf3b1_scripts
Code for alternative splicing analysis of SF3B1 knockdown vs control replicates
griffithlab/sphinxcontrib-images
sphinxcontrib-images extension (moved to https://github.com/sphinx-contrib/images)
griffithlab/sphinxcontrib-programoutput
Sphinx extension for capturing program output