Explore @griffithlab Open Source projects

The Griffith Lab (@griffithlab)

griffithlab

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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.

GenVisR

Genome data visualizations

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

pVAC-Seq

DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools

civic-client

Web client for CIViC: Clinical Interpretations of Variants in Cancer

DeepSVR

Jupyter Notebook

pmbio.org

Website for the precision medicine workshop

civic-server

Backend Server for CIViC Project

rnaseq_tutorial_wiki

The wiki repo, with pull request enabled, for the rnaseq_tutorial

VAtools

A set of tools to annotate VCF files with expression and readcount data

convert_zero_one_based

Python CLI to convert between zero and one based genomic coordinate systems

civic-v2

CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer

genviz.org

Genomic data interpretation and visualization Workshop

igvnav

griffithlab.org

Griffith lab research website

rnaseq_tutorial_v1

Archive of original RNAseq.wiki tutorial that accompanied PLoS Comp Bio paper

civic-meeting

Repo for advertising and organizing CIViC unconference/meeting activities

civicpy

A python interface for the CIViC db application

civic-docs

Source code for the civicdb.org docs

docm

Rails frontend to The Genome Institute's database of curated mutations (DoCM)

anchor_huiming_etal_2023

Code for computational workflows and analyses relating to "Computational prediction of MHC anchor locations guide neoantigen identification and prioritization"

Jupyter Notebook

docker-pvactools

gen-viz-lectures

lectures for genviz.org workshop kept separate for performance

analysis-wdls

Early stages of converting genome/analysis-workflows from CWL to WDL

aml31

Resource website for the AML31 publication

immuno_gcp_wdl_local

Tutorial to run immuno.wdl on Google Cloud

BGA-interface-projects

Monorepo for user-interface projects of the Bioinformatics and Genome Analytics group at MGI

neoag_protocol

Protocol for end-to-end neoantigen analysis and vaccine design for a single patient

CRC_biomarkers

Repo for analysis of CRC biomarkers from stool samples

cloud-workflows

Infrastructure and tooling required to get genomic workflows running in the cloud

civic-panel

Tools for selecting targets for and designing panel for various assays

Jupyter Notebook

ast17

CSHL Advanced Sequencing Technologies and Applications 2017 Course Directory

civic2clinvar

extraction of CIViC variants into the clinvar submission format

bioinformatic-workflows

CWL workflows for bioinformatic analysis

Common Workflow Language