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nucleotide-transformer Public
Forked from instadeepai/nucleotide-transformer🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
Python Other UpdatedMay 26, 2025 -
GENERanno Public
Forked from GenerTeam/GENERannoGENERanno: A Unified Genomic Foundation Model with Specialization in Gene Annotation
Python MIT License UpdatedMay 26, 2025 -
GENERator Public
Forked from GenerTeam/GENERatorGENERator: A Long-Context Generative Genomic Foundation Model
Python MIT License UpdatedMay 26, 2025 -
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multimolecule Public
Forked from DLS5-Omics/multimoleculeAccelerate Molecular Biology Research with Machine Learning
Python GNU Affero General Public License v3.0 UpdatedMay 6, 2025 -
evo Public
Forked from evo-design/evoBiological foundation modeling from molecular to genome scale
Jupyter Notebook Apache License 2.0 UpdatedMay 2, 2025 -
evo2 Public
Forked from ArcInstitute/evo2Genome modeling and design across all domains of life
Jupyter Notebook Apache License 2.0 UpdatedMay 2, 2025 -
LucaOne Public
Forked from LucaOne/LucaOneThe resources of LucaOne, including: the model code, training scripts, embedding inference code, and trained checkpoints.
Python Apache License 2.0 UpdatedMay 2, 2025 -
Awesome-LLMs-meet-genomes Public
Forked from ychuest/Awesome-LLMs-meet-genomesExplore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in genomes.
MIT License UpdatedApr 11, 2025 -
llms-learning Public
Forked from Strivin0311/llms-learningA repository sharing the literatures about large language models
Jupyter Notebook UpdatedApr 11, 2025 -
marsilea Public
Forked from Marsilea-viz/marsileaDeclarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
Python MIT License UpdatedApr 11, 2025 -
gpn Public
Forked from songlab-cal/gpnGenomic Pre-trained Network
Jupyter Notebook MIT License UpdatedApr 10, 2025 -
DNABERT_S Public
Forked from MAGICS-LAB/DNABERT_SDNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models
Python UpdatedApr 7, 2025 -
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genomeocean Public
Forked from jgi-genomeocean/genomeoceanThe official implementation of GenomeOcean.
Python Other UpdatedMar 28, 2025 -
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chrombpnet Public
Forked from kundajelab/chrombpnetBias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
Jupyter Notebook MIT License UpdatedFeb 7, 2025 -
Orthrus Public
Forked from bowang-lab/OrthrusOrthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifically designed for long-sequence data, such as RNA.
Python MIT License UpdatedJan 21, 2025 -
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paper-reading-note Public
Forked from Tramac/paper-reading-note和李沐一起读论文
Apache License 2.0 UpdatedJan 8, 2025 -
single_cell_toolkit Public
Forked from aertslab/single_cell_toolkitTools for correcting single cell barcodes for various scATAC-seq techniques and creating fragment files and spltting BAM files per cluster.
Shell UpdatedJan 6, 2025 -
LBM_Series Public
Forked from ChaozhongLiu/LBM_SeriesLarge Biology Model Introduction Series
Jupyter Notebook UpdatedJan 3, 2025 -
DNABERT_2 Public
Forked from MAGICS-LAB/DNABERT_2[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
Shell Apache License 2.0 UpdatedDec 14, 2024 -
scvi-tools Public
Forked from scverse/scvi-toolsDeep probabilistic analysis of single-cell and spatial omics data
Python BSD 3-Clause "New" or "Revised" License UpdatedDec 13, 2024 -
hadge Public
Forked from theislab/hadgeComprehensive pipeline for donor demultiplexing in single cell
Nextflow MIT License UpdatedDec 2, 2024 -
SComatic Public
Forked from cortes-ciriano-lab/SComaticA tool for detecting somatic variants in single cell data
Python Other UpdatedDec 2, 2024 -
Benchmarking-Single-Cell-Perturbation Public
Forked from xianglin226/Benchmarking-Single-Cell-PerturbationSingle-Cell (Perturbation) Model Library
Apache License 2.0 UpdatedNov 11, 2024 -
enformer-pytorch Public
Forked from lucidrains/enformer-pytorchImplementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
Python MIT License UpdatedOct 9, 2024 -
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