griffithlab/civic-v2

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

Language: TypeScript - Size: 71.2 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 19 - Forks: 4

griffithlab/usp7_scripts

Analysis collaboration with Albert Kim lab - impact of USP7 knockout on splicing

Language: Shell - Size: 11.7 KB - Last synced: 9 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

griffithlab/pVACtools

Language: Python - Size: 349 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 125 - Forks: 57

griffithlab/GenVisR

Genome data visualizations

Language: R - Size: 38 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 202 - Forks: 62

griffithlab/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.

Language: R - Size: 438 MB - Last synced: 15 days ago - Pushed: 12 months ago - Stars: 1,312 - Forks: 616

griffithlab/rnabio.org

website for the rnaseq course

Language: SCSS - Size: 763 MB - Last synced: 22 days ago - Pushed: 23 days ago - Stars: 80 - Forks: 32

griffithlab/civicpy

A python interface for the CIViC db application

Language: Python - Size: 79 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 8 - Forks: 4

griffithlab/rnaseq_tutorial_v1

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

Language: R - Size: 92.3 MB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 12 - Forks: 7

griffithlab/sphinxcontrib-images Fork of spinus/sphinxcontrib-images

sphinxcontrib-images extension (moved to https://github.com/sphinx-contrib/images)

Language: Python - Size: 156 KB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

griffithlab/sphinxcontrib-programoutput Fork of OpenNTI/sphinxcontrib-programoutput

Sphinx extension for capturing program output

Language: Python - Size: 104 KB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

griffithlab/sf3b1_scripts

Code for alternative splicing analysis of SF3B1 knockdown vs control replicates

Language: Shell - Size: 10.7 KB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

griffithlab/saturation-mutagenesis-viz

Shiny app for visualizing functional data from saturation mutagenesis assays (TP53, SMAD4, etc.)

Language: R - Size: 56.6 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

griffithlab/humo

Analysis repo for the humanized mouse project

Language: HTML - Size: 375 KB - Last synced: about 1 month ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

griffithlab/misc-resources

misc

Language: Perl - Size: 77.7 MB - Last synced: about 1 month ago - Pushed: about 8 years ago - Stars: 0 - Forks: 0

griffithlab/igvnav

Language: Python - Size: 73 MB - Last synced: about 1 month ago - Pushed: over 6 years ago - Stars: 15 - Forks: 3

griffithlab/docker-pvactools

Language: Python - Size: 68.4 KB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 3 - Forks: 7

griffithlab/GenVisR-1

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/GenVisR.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=GenVisR.

Language: R - Size: 376 KB - Last synced: about 1 month ago - Pushed: over 8 years ago - Stars: 0 - Forks: 3

griffithlab/docker-civicpy

Docker containerization of the CIViCpy package - https://github.com/griffithlab/civicpy - civicpy.org

Language: Dockerfile - Size: 1000 Bytes - Last synced: about 1 month ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

griffithlab/civic-api-docs Fork of slatedocs/slate

Beautiful static documentation for your API

Language: JavaScript - Size: 999 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 1 - Forks: 3

griffithlab/civic-docs

Source code for the civicdb.org docs

Size: 54.9 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 4 - Forks: 8

griffithlab/docm

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

Language: Ruby - Size: 5.11 MB - Last synced: about 1 month ago - Pushed: over 6 years ago - Stars: 5 - Forks: 5

griffithlab/epics

The project management repo of the Griffith Lab

Size: 2.93 KB - Last synced: about 1 month ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

griffithlab/civic-api-client

Example tools using the CIVIC API

Language: Python - Size: 1.05 MB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 2

griffithlab/civic-meeting

Repo for advertising and organizing CIViC hackathon/meeting activities

Size: 21.5 KB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 10 - Forks: 3

griffithlab/angular-ui-router-civic

Fork of ui-router with fix for uiSrefActive and nested routes applied

Language: JavaScript - Size: 2.37 MB - Last synced: about 1 month ago - Pushed: almost 10 years ago - Stars: 0 - Forks: 0

griffithlab/BGA-interface-projects

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

Language: TypeScript - Size: 847 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 1 - Forks: 3

griffithlab/ast17

CSHL Advanced Sequencing Technologies and Applications 2017 Course Directory

Language: CSS - Size: 129 KB - Last synced: about 1 month ago - Pushed: over 6 years ago - Stars: 1 - Forks: 20

griffithlab/aml31

Resource website for the AML31 publication

Language: CSS - Size: 34.1 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 2 - Forks: 1

griffithlab/genviz.org

Genomic data interpretation and visualization Workshop

Language: SCSS - Size: 226 MB - Last synced: about 1 month ago - Pushed: 11 months ago - Stars: 18 - Forks: 4

griffithlab/regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.

Language: C++ - Size: 6.06 MB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 110 - Forks: 24

griffithlab/DeepImmuno Fork of frankligy/DeepImmuno

Deep-learning empowered prediction and generation of immunogenic epitopes for T cell immunity

Language: Jupyter Notebook - Size: 34.9 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 2 - Forks: 0

griffithlab/bioinformatic-workflows

CWL workflows for bioinformatic analysis

Language: Common Workflow Language - Size: 70.3 KB - Last synced: about 1 month ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 3

griffithlab/bigmhc Fork of KarchinLab/bigmhc

BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity

Language: Jupyter Notebook - Size: 2.31 GB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

griffithlab/VAtools

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

Language: Python - Size: 38.8 MB - Last synced: 26 days ago - Pushed: 4 months ago - Stars: 24 - Forks: 10

griffithlab/docker-vatools

Language: Dockerfile - Size: 17.6 KB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 0 - Forks: 1

griffithlab/civic2clinvar

extraction of CIViC variants into the clinvar submission format

Language: Python - Size: 11.7 KB - Last synced: 3 days ago - Pushed: about 5 years ago - Stars: 1 - Forks: 1

griffithlab/rnaseq_tutorial_wiki

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

Language: Perl - Size: 446 MB - Last synced: about 1 month ago - Pushed: about 4 years ago - Stars: 25 - Forks: 22

griffithlab/pVAC-Seq

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

Language: Python - Size: 15.6 MB - Last synced: 28 days ago - Pushed: about 5 years ago - Stars: 60 - Forks: 48

griffithlab/convert_zero_one_based

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

Language: Python - Size: 33.2 KB - Last synced: about 1 month ago - Pushed: almost 6 years ago - Stars: 21 - Forks: 6

griffithlab/neoag_vaccine_scripts

Language: Python - Size: 138 KB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

griffithlab/DeepSVR

Language: Jupyter Notebook - Size: 162 MB - Last synced: about 1 month ago - Pushed: almost 5 years ago - Stars: 49 - Forks: 19

griffithlab/civic-client

Web client for CIViC: Clinical Interpretations of Variants in Cancer

Language: JavaScript - Size: 28 MB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 50 - Forks: 28

griffithlab/anchor_huiming_etal_2023

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

Language: Jupyter Notebook - Size: 83.7 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 5 - Forks: 0

griffithlab/griffithlab.org

Griffith lab research website

Language: JavaScript - Size: 182 MB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 14 - Forks: 27

griffithlab/pmbio.org

Website for the precision medicine workshop

Language: SCSS - Size: 272 MB - Last synced: about 1 month ago - Pushed: 9 months ago - Stars: 41 - Forks: 19

griffithlab/Immuno_Workflow_Course

Language: CSS - Size: 8.17 MB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 0 - Forks: 1

griffithlab/pVACtools_Intro_Course

Getting started with pVACtools - pVACseq, pVACbind and pVACview

Language: CSS - Size: 101 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 0 - Forks: 2

griffithlab/DeepNeo Fork of kaistomics/DeepNeo

identification of immunogenic neoepitopes

Size: 2.13 MB - Last synced: about 1 month ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

griffithlab/CIVIC_SVI_Course

A hands on course explaining how to complete somatic cancer variant interpretation using CIViC and current guidelines

Language: CSS - Size: 69.2 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 0 - Forks: 2

griffithlab/civic-server

Backend Server for CIViC Project

Language: HTML - Size: 190 MB - Last synced: about 1 month ago - Pushed: 11 months ago - Stars: 39 - Forks: 32

griffithlab/precision_medicine_KISC

This is the precision medicine KISC site/lab manual

Size: 0 Bytes - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

griffithlab/gen-viz-lectures

lectures for genviz.org workshop kept separate for performance

Size: 521 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 3 - Forks: 1

griffithlab/itcr2022

Jekyll site for ITCR 2022 conference

Language: HTML - Size: 34.7 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

griffithlab/civic-mapper

Tool to map variants to CIViC entries

Language: Python - Size: 22.5 KB - Last synced: about 1 month ago - Pushed: almost 8 years ago - Stars: 0 - Forks: 0

griffithlab/cancer-hotspots

Predicting neoantigens from cancer hotspots

Language: R - Size: 82 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

griffithlab/open-data-registry Fork of awslabs/open-data-registry

A registry of publicly available datasets on AWS

Language: Python - Size: 1.59 MB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

griffithlab/brain-tumor-heterogeneity

Code for figures

Language: R - Size: 16.7 MB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

griffithlab/civic-panel

Tools for selecting targets for and designing panel for various assays

Language: Jupyter Notebook - Size: 82.4 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 3

griffithlab/MCL_project

Scripts used for the MCL data pipeline

Language: Shell - Size: 15.6 KB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

griffithlab/saturation-mutagenesis-website

Companion website to the saturation mutagenesis toolkit

Language: HTML - Size: 5.71 MB - Last synced: about 1 month ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

griffithlab/command_line_bootcamp Fork of command-line-bootcamp/cli-boot.camp

:computer: command-line bootcamp adventure in your browser

Language: JavaScript - Size: 1.27 MB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

griffithlab/neoag_protocol

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

Size: 1000 Bytes - Last synced: about 1 month ago - Pushed: about 4 years ago - Stars: 1 - Forks: 0

griffithlab/genvisr.org

Companion website for the GenVisR library

Language: HTML - Size: 12.8 MB - Last synced: about 1 month ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

griffithlab/jekyll_template

Work to enhance existing jekyll sites

Size: 1000 Bytes - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

griffithlab/CIViC_PM

Open-sourced Precision Medicine Pathway using CIViC Annotations

Language: HTML - Size: 3.55 MB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

griffithlab/CRC_biomarkers

Repo for analysis of CRC biomarkers from stool samples

Size: 70.1 MB - Last synced: about 1 month ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 2

griffithlab/gnomad_annotation

Python package to add gnomAD allele frequencies to MGI annotated files

Language: Python - Size: 146 KB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 0 - Forks: 1

griffithlab/regtools-cwl

cwl workflow for running regtools

Language: Common Workflow Language - Size: 26.4 KB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 0 - Forks: 1

griffithlab/toil_aws_setup

Instructions for setting up to run Toil on AWS

Size: 1000 Bytes - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

griffithlab/bioconda-recipes Fork of bioconda/bioconda-recipes

Conda recipes for the bioconda channel.

Language: Shell - Size: 149 MB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

griffithlab/civic-curation

For CIViC curation issues that do not directly involve code changes

Size: 1000 Bytes - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

griffithlab/pvac-seq-client

browser client for the pVAC-Seq project

Language: CSS - Size: 1.54 MB - Last synced: 22 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 2