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eTheRNA immunotherapies

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https://www.etherna.be/

Rajendra Bahadur Shahi's repositories

hugo

The world’s fastest framework for building websites.

Language:GoApache-2.01 10

pytorch-styleguide

An unofficial styleguide and best practices summary for PyTorch

Language:PythonGPL-3.0100

somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq

Language:ShellBSD-2-Clause1 20

STAR

RNA-seq aligner

Language:CNOASSERTION1 20

antigen.garnish

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

Language:RNOASSERTION010

gatk

Official code repository for GATK versions 4 and up

Language:JavaBSD-3-Clause010

Awesome-pytorch-list

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

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Awsome_Deep_Geometry_Learning

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

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bamsurgeon

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

Language:PythonMIT010

bcbio-nextgen

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

Language:PythonMIT010

Codon-optimization

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

Language:PythonMIT000

Codon-Optimization-1

A neural based approach to the task of genetic codon optimization

Language:Jupyter Notebook000

datawarrior

Interactive data analysis and visualisation with chemical intelligence

Language:JavaGPL-3.0000

DeCOIL

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

Language:Jupyter Notebook010

DeepTAP

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

Language:PythonApache-2.0000

fishplot

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

Language:RNOASSERTION020

fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data

Language:PythonGPL-3.0010

GeoDiff

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

Language:PythonMIT000

HLAminer

⛏HLA predictions from NGS shotgun data

Language:PerlNOASSERTION010

mhctools

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

Language:PythonApache-2.0020

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.

Language:JavaNOASSERTION020

neusomatic

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection

Language:PythonNOASSERTION010

OPERA

Free and open-source application (command line and GUI) providing QSAR models predictions as well as applicability domain and accuracy assessment for physicochemical properties, environmental fate and toxicological endpoints. ==================>Download the latest compiled version from the "releases" tab and run the executable installer.

Language:MATLABMIT000

Promotech

Machine-learning-based general bacterial promoter prediction tool.

Language:CGPL-3.0000

pytorch-tutorial

PyTorch Tutorial for Deep Learning Researchers

Language:PythonMIT000

retained-intron-neoantigen-pipeline

Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.

Language:PythonApache-2.0010

rnafusion

RNA-seq analysis pipeline for detection gene-fusions

Language:NextflowMIT010

SAMPL8

Challenge details, inputs, and (eventually) results for the SAMPL8 series of challenges

Language:PythonMIT000

snakemake-gatk

:snake::wrench: Snakemake wrappers for GATK.

Language:Python010

VAtools

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

Language:PythonMIT010