Alternatives and similar repositories for genomic-FM

Users that are interested in genomic-FM are comparing it to the libraries listed below

• aaronwtr / PertEval
  Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.
  ☆25Updated 2 months ago
• microsoft / zero-shot-scfoundation
  ☆64Updated 9 months ago
• DeepGraphLearning / scCello
  [NeurIPS 2024 Spotlight] A cell-ontology guided transcriptome foundation model
  ☆15Updated 2 months ago
• jimmylihui / GenBench
  ☆21Updated 3 months ago
• rahuldhodapkar / cell2sentence
  Create cell sentences from sequencing data
  ☆22Updated 9 months ago
• bowang-lab / Orthrus
  Orthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifical…
  ☆65Updated 4 months ago
• Genentech / iterative-perturb-seq
  Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors
  ☆40Updated last year
• snap-stanford / KGWAS
  KGWAS: novel genetics discovery enabled by massive functional genomics knowledge graph
  ☆69Updated 2 months ago
• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆39Updated 8 months ago
• HakimBenkirane / CustOmics
  A deep-learning framework for multi-omics integration
  ☆26Updated last year
• kundajelab / DART-Eval
  ☆34Updated last month
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆31Updated 2 months ago
• genbio-ai / ModelGenerator
  AIDO.ModelGenerator is a software stack powering the development of an AI-driven Digital Organism (AIDO) by enabling researchers to adapt…
  ☆61Updated 3 weeks ago
• OmicsML / CellPLM
  Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
  ☆85Updated last year
• carpenter-singh-lab / 2022_Haghighi_NatureMethods
  High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
  ☆48Updated 4 months ago
• bowang-lab / IntegrAO
  Integrate Any Omics: Towards genome-wide data integration for patient stratification
  ☆53Updated 2 weeks ago
• theislab / CellFlow
  Modeling complex perturbations with CellFlow
  ☆49Updated this week
• dohlee / chromoformer
  The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
  ☆35Updated last year
• snap-stanford / BioDiscoveryAgent
  BioDiscoveryAgent is an LLM-based AI agent for closed-loop design of genetic perturbation experiments
  ☆72Updated 2 weeks ago
• TencentAILabHealthcare / DNAGPT
  ☆39Updated last year
• aristoteleo / awesome-bioagent-papers
  Agent self-driven repository on bio-agent papers, i.e. papers on LLM-based agents in biology and medicine.
  ☆42Updated this week
• instadeepai / multiomics-open-research
  BulkRNABert: Cancer prognosis from bulk RNA-seq based language models
  ☆24Updated 10 months ago
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆19Updated 11 months ago
• HelloWorldLTY / scEval
  Codes for paper: Evaluating the Utilities of Large Language Models in Single-cell Data Analysis.
  ☆70Updated 4 months ago
• clinicalml / sc-foundation-eval
  Code for evaluating single cell foundation models scBERT and scGPT
  ☆43Updated 9 months ago
• mims-harvard / PINNACLE
  Contextual AI models for single-cell protein biology
  ☆87Updated 3 months ago
• jsxlei / scCLIP
  ☆28Updated last year
• OmicsML / scDiff
  scDiff: A General Single-Cell Analysis Framework via Conditional Diffusion Generative Models
  ☆28Updated 9 months ago
• EperLuo / scDiffusion
  A model developed for the generation of scRNA-seq data
  ☆64Updated 3 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆56Updated 2 weeks ago