johapark

johapark's Stars

• google/deepsomatic

  DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

  11715

• Daniel-Liu-c0deb0t/block-aligner

  SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

  Language:Jupyter Notebook1246

• facebookresearch/esm

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

  Language:Python3.1k615

• mrvollger/SmkTemplate

  A template repository for snakemake workflows.

  Language:Python331

• mrvollger/rustybam

  bioinformatics toolkit in rust

  Language:Rust782

• sstadick/perbase

  Per-base per-nucleotide depth analysis

  Language:Rust11513

• PacificBiosciences/trgt

  Tandem repeat genotyping and visualization from PacBio HiFi data

  Language:Rust977

• shenwei356/seqkit

  A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

  Language:Go1.3k157

• vgteam/vg

  tools for working with genome variation graphs

  Language:C++1.1k193

• snakemake-workflows/rna-seq-star-deseq2

  RNA-seq workflow using STAR and DESeq2

  Language:Python319196

• evo-design/evo

  Biological foundation modeling from molecular to genome scale

  Language:Jupyter Notebook915108

• waveygang/wfmash

  base-accurate DNA sequence alignments using WFA and mashmap3

  Language:C++17416

• chanzuckerberg/cellxgene-census

  CZ CELLxGENE Discover Census

  Language:Jupyter Notebook7720

• 38/d4-format

  The D4 Quantitative Data Format

  Language:Rust15220

• zillow/quantile-forest

  Quantile Regression Forests compatible with scikit-learn.

  Language:Python18522

• meta-llama/codellama

  Inference code for CodeLlama models

  Language:Python15.8k1.8k

• mtdvio/every-programmer-should-know

  A collection of (mostly) technical things every software developer should know about

  82k7.7k

• ENCODE-DCC/atac-seq-pipeline

  ENCODE ATAC-seq pipeline

  Language:Python380171

• rapidfuzz/Levenshtein

  The Levenshtein Python C extension module contains functions for fast computation of Levenshtein distance and string similarity

  Language:C++26416

• rapidfuzz/python-Levenshtein

  The Levenshtein Python C extension module contains functions for fast computation of Levenshtein distance and string similarity

  904

• marcelm/dnaio

  Efficiently read and write sequencing data from Python

  Language:Python618

• google-deepmind/alphamissense

  Language:Python48964

• cmdcolin/awesome-genome-visualization

  A list of interesting genome browser or genome-browser-like implementations

  Language:TypeScript813105

• google/comprehensive-rust

  This is the Rust course used by the Android team at Google. It provides you the material to quickly teach Rust.

  Language:Rust27.4k1.6k

• pachterlab/gget

  🧬 gget enables efficient querying of genomic reference databases

  Language:Python91472

• pola-rs/polars

  Dataframes powered by a multithreaded, vectorized query engine, written in Rust

  Language:Rust29k1.8k

• scverse/squidpy

  Spatial Single Cell Analysis in Python

  Language:Python41876

• InsightSoftwareConsortium/SimpleITK-Notebooks

  Jupyter notebooks for learning how to use SimpleITK

  Language:Jupyter Notebook827348

• pyushkevich/greedy

  Very fast greedy diffeomorphic registration code

  Language:C++6117

• InsightSoftwareConsortium/ITKElastix

  An ITK Python interface to elastix, a toolbox for rigid and nonrigid registration of images

  Language:Python19922