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alphafold

Open source code for AlphaFold.

alphamissense

als-deeplearning

Deep learning frame for genetic disease

als-gene-network-manuscript

als_pathways

This repository contains the programming codes used in Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types https://advances.sciencemag.org/content/7/3/eabd9036

alsgenescanner

annotsv

Annotation and Ranking of Structural Variation

benchmarking-tools

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

biobert

Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining

biobert-pretrained

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

clinvcf

Generate an enhanced VCF files from ClinVar XML Full releases

deep-loop

Identification of chromatin loops using deep learning

deepbind

I have put my modified version of the deepbind code here.

deepbindtokeras

Convert DeepBind models to Keras

deepsvfilter

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

dexseq

django-webapp

This is a web-app created using Python, Django. By using this user can login, upload files and also can view and download files uploaded by other users.

dnashaper

R package for high-throughput DNA shape predictions and feature encoding

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

esm-variants

ga4k

We are working hard to make progress for patients with genetic disease!

gatk

Official code repository for GATK versions 4 and up

gatk4-exome-analysis-pipeline

This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.

gatk4-genome-processing-pipeline

Workflows used for processing whole genome sequence data + germline variant calling.

gatk4-germline-snps-indels

Workflows for germline short variant discovery with GATK4

genomealert_app

Shiny app of Genome Alert! explorations.

gentrl

Generative Tensorial Reinforcement Learning (GENTRL) model

gofuncr

R-package for GO-enrichment analyses

gopca

GO-PCA: An Unsupervised Method to Explore Gene Expression Data Using Prior Knowledge