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.
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.
facebookresearch/esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
mrvollger/SmkTemplate
A template repository for snakemake workflows.
mrvollger/rustybam
bioinformatics toolkit in rust
sstadick/perbase
Per-base per-nucleotide depth analysis
PacificBiosciences/trgt
Tandem repeat genotyping and visualization from PacBio HiFi data
shenwei356/seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
vgteam/vg
tools for working with genome variation graphs
snakemake-workflows/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
evo-design/evo
Biological foundation modeling from molecular to genome scale
waveygang/wfmash
base-accurate DNA sequence alignments using WFA and mashmap3
chanzuckerberg/cellxgene-census
CZ CELLxGENE Discover Census
38/d4-format
The D4 Quantitative Data Format
zillow/quantile-forest
Quantile Regression Forests compatible with scikit-learn.
meta-llama/codellama
Inference code for CodeLlama models
mtdvio/every-programmer-should-know
A collection of (mostly) technical things every software developer should know about
ENCODE-DCC/atac-seq-pipeline
ENCODE ATAC-seq pipeline
rapidfuzz/Levenshtein
The Levenshtein Python C extension module contains functions for fast computation of Levenshtein distance and string similarity
rapidfuzz/python-Levenshtein
The Levenshtein Python C extension module contains functions for fast computation of Levenshtein distance and string similarity
marcelm/dnaio
Efficiently read and write sequencing data from Python
google-deepmind/alphamissense
cmdcolin/awesome-genome-visualization
A list of interesting genome browser or genome-browser-like implementations
google/comprehensive-rust
This is the Rust course used by the Android team at Google. It provides you the material to quickly teach Rust.
pachterlab/gget
š§¬ gget enables efficient querying of genomic reference databases
pola-rs/polars
Dataframes powered by a multithreaded, vectorized query engine, written in Rust
scverse/squidpy
Spatial Single Cell Analysis in Python
InsightSoftwareConsortium/SimpleITK-Notebooks
Jupyter notebooks for learning how to use SimpleITK
pyushkevich/greedy
Very fast greedy diffeomorphic registration code
InsightSoftwareConsortium/ITKElastix
An ITK Python interface to elastix, a toolbox for rigid and nonrigid registration of images