josephhalstead

josephhalstead's Stars

• Significant-Gravitas/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.

  Language:Python170k1.5k3.1k44.7k

• 3b1b/manim

  Animation engine for explanatory math videos

  Language:Python73.5k9091.2k6.4k

• run-llama/llama_index

  LlamaIndex is a data framework for your LLM applications

  Language:Python37.8k2505.7k5.4k

• Edinburgh-Genome-Foundry/DnaFeaturesViewer

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

  Language:Python608197493

• PapenfussLab/gridss

  GRIDSS: the Genomic Rearrangement IDentification Software Suite

  Language:Java2602266071

• google/deepconsensus

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

  Language:Python232176935

• exomiser/Exomiser

  A Tool to Annotate and Prioritize Exome Variants

  Language:Java2032451055

• codota/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

  Language:Python197177137

• rust-bio/rust-bio-tools

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

  Language:Rust189253823

• brentp/echtvar

  using all the bits for echt rapid variant annotation and filtering

  Language:Rust14753110

• sstadick/perbase

  Per-base per-nucleotide depth analysis

  Language:Rust12264616

• varlociraptor/varlociraptor

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

  Language:Rust12276916

• olivettigroup/article-downloader

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

  Language:Python11917933

• Illumina/PrimateAI

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

  Language:Python11325630

• zeeev/wham

  Structural variant detection and association testing

  Language:C++104194825

• mbhall88/ssubmit

  Submit slurm sbatch jobs without a script

  Language:Rust65245

• OATML/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.

  Language:Python638854

• brentp/rare-disease-wf

  (WIP) best-practices workflow for rare disease

  Language:Nextflow598108

• sigven/cpsr

  Cancer Predisposition Sequencing Reporter (CPSR)

  Language:R5874312

• GooglingTheCancerGenome/sv-channels

  Deep learning-based structural variant filtering method

  Language:Python375805

• Illumina/GraphAlignmentViewer

  Language:Python3511710

• Illumina/witty.er

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

  Language:C#30571

• dellytools/sansa

  Structural variant VCF annotation, duplicate removal and comparison

  Language:C++28361

• andrewSharo/StrVCTVRE

  StrVCTVRE, a structural variant classifier for exonic deletions and duplications

  Language:Jupyter Notebook18496

• ccmbioinfo/crg2

  Research pipeline for exploring clinically relevant genomic variants

  Language:Python177825

• elzbth/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.

  Language:Python175238

• ailabstw/variant2literature

  Language:Python15215

• bahlolab/Genes4Epilepsy

  A curated list of monogenic epilepsy genes

  Language:HTML10601

• brentp/sveval

  run multiple sv evalution tools

  Language:Python840

• queenjobo/PhaseMyDeNovo

  Script for phasing DNMs

  Language:Python61