zhpan99

shiny

Easy interactive web applications with R

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

GenVisR

Genome data visualizations

learning_bam_file

Learning the Sequence Alignment/Map format

Repo-2016

R, Python and Mathematica Codes in Machine Learning, Deep Learning, Artificial Intelligence, NLP and Geolocation

mutect

MuTect -- Accurate and sensitive cancer mutation detection

mhctools

Python interface to running command-line and web-based MHC binding predictors

guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly

varcode

Library for manipulating genomic variants and predicting their effects

oncotator

pVAC-Seq

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 This tool has been superseded by https://github.com/griffithlab/pVACtools

EVmutation

Mutation effects predicted from sequence co-variation

vaxrank

Ranked vaccine peptides for personalized cancer immunotherapy

pepdata

Python interface to amino acid properties and IEDB

single_cell_portal

Tutorials, workflows, and convenience scripts for Single Cell Portal

epidisco

Personalized cancer epitope discovery and peptide vaccine prediction pipeline

topiary

Predict mutated T-cell epitopes from sequencing data

myvariant.py

Python client for MyVariant.info web services.

cohorts

Utilities for analyzing mutations and neoepitopes in patient cohorts

pygdc

Python API for Genomic Data Commons

awesome-clonality

A curated list of awesome clonality and tumor heterogeneity resources

immuno

Use somatic mutations to choose a personalized cancer vaccine (tumor-specific immunogenic peptides)

vcf-annotate-polyphen

A tool to annotate human VCF files with PolyPhen2 effect measures

MuTest

A prototype database for storing somatic variants.

bcbb

Useful bioinformatics code, primarily in Python and R

immuno_research

Predicting immunogenicity of short peptides

topeology

Compare neoepitope sequences with epitopes from IEDB

Neoepitope_Prediction

imseq

IMSEQ - IMmunogenetic SEQuence Analysis