Single-cell analysis in Python. Scales to >100M cells.
- machine-learning
- data-science
- visualize-data
- transcriptomics
Repository Index
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Reverse engineering SARS-CoV-2
- covid-19
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
- fastq
- qc
- preprocessing
- filtering
A versatile pairwise aligner for genomic and spliced nucleotide sequences
- bioinformatics
- sequence-alignment
- spliced-alignment
- genomics
Official code repository for GATK versions 4 and up
Deep probabilistic analysis of single-cell and spatial omics data
- scrna-seq
- variational-bayes
- variational-autoencoder
- cite-seq
Implementation of Alphafold 3 from Google Deepmind in Pytorch
- artificial-intelligence
- deep-learning
- attention-mechanisms
- denoising-diffusion
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.
- ai-agents
- bioinformatics
- equity
- genomics
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
- dna
- k-mer
- python
- bloom-filter
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
- kmer
- dnabert-model
- kmer-format
- gpu
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
Spatial Single Cell Analysis in Python
- single-cell-rna-seq
- single-cell-genomics
- spatial-transcriptomics
- spatial-analysis
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
talk with NCBI entrez using R
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
LLM for Drug Editing, ICLR 2024
- chatgpt
- conversation
- drug
- drug-discovery
TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524
- self-attention
- compound-protein-interaction
- transformercpi
- structure-free-virtual-sreening
NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
- r
- neuroanatomy-toolbox
- cran
- neuron
Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders
- epigenomics
- pattern-search
- data-visualization
- interactive-machine-learning
Run scripts, explore your genome, and get personalized explanations — all in natural dialogue.
- analysis
- claude
- claudecode
- dna