josephhalstead

article-downloader

Uses publisher APIs to programmatically retrieve scientific journal articles for text mining.

StrVCTVRE

StrVCTVRE, a structural variant classifier for exonic deletions and duplications

variant2literature

AutoGPT

AutoGPT is the vision of accessible AI for everyone, to use and to build on. Our mission is to provide the tools, so that you can focus on what matters.

Genes4Epilepsy

A curated list of monogenic epilepsy genes

llama_index

LlamaIndex is a data framework for your LLM applications

ssubmit

Submit slurm sbatch jobs without a script

Exomiser

A Tool to Annotate and Prioritize Exome Variants

sansa

Structural variant VCF annotation, duplicate removal and comparison

echtvar

using all the bits for echt rapid variant annotation and filtering

manim

Animation engine for explanatory math videos

GraphAlignmentViewer

EVE

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.

crg2

Research pipeline for exploring clinically relevant genomic variants

wham

Structural variant detection and association testing

deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite

sveval

run multiple sv evalution tools

varlociraptor

Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.

cpsr

Cancer Predisposition Sequencing Reporter (CPSR)

rare-disease-wf

(WIP) best-practices workflow for rare disease

sv-channels

Deep learning-based structural variant filtering method

PhaseMyDeNovo

Script for phasing DNMs

witty.er

What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.

jitterbug

Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.

tabnine-sublime

Tabnine Autocomplete AI: JavaScript, Python, TypeScript, PHP, C/C++, HTML/CSS, Go, Java, Ruby, C#, Rust, SQL, Bash, Kotlin, Julia, Lua, OCaml, Perl, Haskell, React

rust-bio-tools

A set of command line utilities based on Rust-Bio.

perbase

Per-base per-nucleotide depth analysis

DnaFeaturesViewer

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

PrimateAI

deep residual neural network for classifying the pathogenicity of missense mutations.