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antigen.garnish

Ensemble Antigen Prediction and Quality Analysis from DNA Variants and Proteins in R

awesome-algorithms

A curated list of awesome places to learn and/or practice algorithms.

awesome-pytorch-list

A comprehensive list of pytorch related content on github,such as different models,implementations,helper libraries,tutorials etc.

awsome_deep_geometry_learning

A list of resources about deep learning solutions on 3D shape processing

bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

benchmarking-tools

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

bigmart-sales-prediction-analyticsvidya

solution to the question Big mart sales prediction

cerebro-paper

codon-optimization

Use machine learning to design codon-optimized DNA sequences for increased protein expression.

codon-optimization-1

A neural based approach to the task of genetic codon optimization

datawarrior

Interactive data analysis and visualisation with chemical intelligence

decoil

A computational method to optimize degenerate codons for synthesizing an informed combinatorial mutagenesis protein variant library

deeptap

TAPPred is a deep learning approach used for predicting high-confidence TAP-binding peptide.

dna-seq-analysis

DNA sequencing analysis notes from Ming Tang

epidisco

Personalized cancer epitope discovery and peptide vaccine prediction pipeline

fishplot

Create timecourse "fish plots" that show changes in the clonal architecture of tumors

fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data

gatk

Official code repository for GATK versions 4 and up

geodiff

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

hlaminer

⛏HLA predictions from NGS shotgun data

hugo

The world’s fastest framework for building websites.

hugo-academic

The website designer for Hugo. Build and deploy a beautiful website in minutes :rocket:

kallisto

Near-optimal RNA-Seq quantification

ketrew

Keep Track of Experimental Workflows

mhctools

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

mixcr

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

mupexi

MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.

mutation-signatures

Create mutation signatures from MAF's, and decompose them into Stratton signatures

mutect2_snakemake

Run GAKT's MuTect2 using Snakemake