Pinned Repositories
pVACtools
antigen.garnish
Ensemble Antigen Prediction and Quality Analysis from DNA Variants and Proteins in R
gatk
Official code repository for GATK versions 4 and up
hugo
The world’s fastest framework for building websites.
kallisto
Near-optimal RNA-Seq quantification
pipeline-example
example ruffus pipeline
pytorch-styleguide
An unofficial styleguide and best practices summary for PyTorch
rubra
Infrastructure code to support DNA pipeline
STAR
RNA-seq aligner
strelka
Strelka2 germline and somatic small variant caller
ShahiRB's Repositories
ShahiRB/hugo
The world’s fastest framework for building websites.
ShahiRB/pytorch-styleguide
An unofficial styleguide and best practices summary for PyTorch
ShahiRB/somaticseq
An ensemble approach to accurately detect somatic mutations using SomaticSeq
ShahiRB/STAR
RNA-seq aligner
ShahiRB/antigen.garnish
Ensemble Antigen Prediction and Quality Analysis from DNA Variants and Proteins in R
ShahiRB/gatk
Official code repository for GATK versions 4 and up
ShahiRB/Awesome-pytorch-list
A comprehensive list of pytorch related content on github,such as different models,implementations,helper libraries,tutorials etc.
ShahiRB/Awsome_Deep_Geometry_Learning
A list of resources about deep learning solutions on 3D shape processing
ShahiRB/bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
ShahiRB/bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
ShahiRB/Codon-optimization
Use machine learning to design codon-optimized DNA sequences for increased protein expression.
ShahiRB/Codon-Optimization-1
A neural based approach to the task of genetic codon optimization
ShahiRB/datawarrior
Interactive data analysis and visualisation with chemical intelligence
ShahiRB/DeCOIL
A computational method to optimize degenerate codons for synthesizing an informed combinatorial mutagenesis protein variant library
ShahiRB/DeepTAP
TAPPred is a deep learning approach used for predicting high-confidence TAP-binding peptide.
ShahiRB/fishplot
Create timecourse "fish plots" that show changes in the clonal architecture of tumors
ShahiRB/fusioncatcher
Finder of Somatic Fusion Genes in RNA-seq data
ShahiRB/GeoDiff
Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).
ShahiRB/HLAminer
⛏HLA predictions from NGS shotgun data
ShahiRB/IRF
Inverted Repeats Finder: a program to analyze DNA and RNA sequences
ShahiRB/mhctools
Python interface to running command-line and web-based MHC binding predictors
ShahiRB/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.
ShahiRB/neusomatic
NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
ShahiRB/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.
ShahiRB/Promotech
Machine-learning-based general bacterial promoter prediction tool.
ShahiRB/pytorch-tutorial
PyTorch Tutorial for Deep Learning Researchers
ShahiRB/retained-intron-neoantigen-pipeline
Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.
ShahiRB/rnafusion
RNA-seq analysis pipeline for detection gene-fusions
ShahiRB/SAMPL8
Challenge details, inputs, and (eventually) results for the SAMPL8 series of challenges
ShahiRB/VAtools
A set of tools to annotate VCF files with expression and readcount data