Alternatives and similar repositories for scGPT

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

• OmicsML / awesome-deep-learning-single-cell-papers
  ☆826Updated 7 months ago
• biomap-research / scFoundation
  ☆373Updated 3 weeks ago
• instadeepai / nucleotide-transformer
  Foundation Models for Genomics & Transcriptomics
  ☆747Updated last month
• scverse / scvi-tools
  Deep probabilistic analysis of single-cell and spatial omics data
  ☆1,514Updated this week
• ArcInstitute / arc-virtual-cell-atlas
  Arc Virtual Cell Atlas
  ☆466Updated 7 months ago
• theislab / single-cell-transformer-papers
  ☆336Updated 6 months ago
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆1,075Updated last month
• yiqunchen / GenePT
  ☆297Updated last year
• OmicsML / awesome-foundation-model-single-cell-papers
  ☆370Updated last week
• TencentAILabHealthcare / scBERT
  ☆339Updated 2 years ago
• Starlitnightly / omicverse
  A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
  ☆796Updated this week
• MAGICS-LAB / DNABERT_2
  [ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
  ☆439Updated 3 months ago
• gao-lab / GLUE
  Graph-linked unified embedding for single-cell multi-omics data integration
  ☆438Updated last month
• theislab / single-cell-tutorial
  Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…
  ☆1,534Updated 3 years ago
• google-deepmind / alphamissense
  ☆598Updated last year
• snap-stanford / GEARS
  GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
  ☆318Updated 10 months ago
• owkin / PyDESeq2
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
  ☆709Updated last week
• jerryji1993 / DNABERT
  DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
  ☆719Updated 5 months ago
• HazyResearch / hyena-dna
  Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
  ☆740Updated 7 months ago
• ArcInstitute / state
  State is a machine learning model that predicts cellular perturbation response across diverse contexts
  ☆472Updated this week
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆760Updated 2 weeks ago
• snap-stanford / UCE
  UCE is a zero-shot foundation model for single-cell gene expression data
  ☆231Updated 9 months ago
• calico / basenji
  Sequential regulatory activity predictions with deep convolutional neural networks.
  ☆459Updated 6 months ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆454Updated last year
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆677Updated 3 weeks ago
• lucidrains / enformer-pytorch
  Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
  ☆546Updated 5 months ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆403Updated 11 months ago
• scverse / scanpy
  Single-cell analysis in Python. Scales to >100M cells.
  ☆2,283Updated this week
• google-deepmind / alphagenome
  This API provides programmatic access to the AlphaGenome model developed by Google DeepMind.
  ☆1,336Updated this week
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆477Updated last week