Alternatives and similar repositories for DNABERT_2

Users that are interested in DNABERT_2 are comparing it to the libraries listed below

• jerryji1993 / DNABERT
  DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
  ☆682Updated last month
• ml4bio / RNA-FM
  Nature Methods: RNA foundation model (together with RhoFold)
  ☆289Updated 2 months ago
• songlab-cal / gpn
  Genomic Pre-trained Network
  ☆273Updated 3 weeks ago
• instadeepai / nucleotide-transformer
  Foundation Models for Genomics & Transcriptomics
  ☆673Updated 3 weeks ago
• MAGICS-LAB / DNABERT_S
  [ISMB 2025] DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models
  ☆107Updated 6 months ago
• ML-Bioinfo-CEITEC / genomic_benchmarks
  Benchmarks for classification of genomic sequences
  ☆150Updated last week
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆185Updated last month
• biomap-research / scFoundation
  ☆348Updated 6 months ago
• Genentech / gReLU
  gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
  ☆269Updated last month
• google-deepmind / alphamissense
  ☆581Updated last year
• TencentAILabHealthcare / scBERT
  ☆320Updated last year
• OATML-Markslab / EVE
  Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…
  ☆177Updated last year
• calico / basenji
  Sequential regulatory activity predictions with deep convolutional neural networks.
  ☆443Updated 2 months ago
• TencentAILabHealthcare / DNAGPT
  ☆43Updated last year
• apeterswu / Awesome-Bio-Foundation-Models
  A collection of awesome bio-foundation models, including protein, RNA, DNA, gene, single-cell, and so on.
  ☆245Updated 2 months ago
• theislab / single-cell-transformer-papers
  ☆323Updated 2 months ago
• jkobject / geneformer
  ☆75Updated 2 months ago
• LucaOne / LucaOne
  The resources of LucaOne, including: the model code, training scripts, embedding inference code, and trained checkpoints.
  ☆291Updated this week
• jimmylihui / GenBench
  ☆22Updated 2 months ago
• ychuest / Awesome-LLMs-meet-genomes
  Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…
  ☆77Updated last week
• steineggerlab / foldseek
  Foldseek enables fast and sensitive comparisons of large structure sets.
  ☆1,018Updated last week
• ArcInstitute / state
  State is a machine learning model that predicts cellular perturbation response across diverse contexts
  ☆302Updated this week
• HazyResearch / hyena-dna
  Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
  ☆705Updated 3 months ago
• lucidrains / enformer-pytorch
  Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
  ☆512Updated last month
• yiqunchen / GenePT
  ☆276Updated last year
• nadavbra / protein_bert
  ☆542Updated 4 months ago
• ArcInstitute / arc-virtual-cell-atlas
  Arc Virtual Cell Atlas
  ☆386Updated 3 months ago
• LinearDesignSoftware / LinearDesign
  The LinearDesign mRNA design software.
  ☆189Updated last year
• bowang-lab / scGPT
  ☆1,295Updated last month
• snap-stanford / GEARS
  GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
  ☆279Updated 6 months ago