Alternatives and similar repositories for awesome-AI4SingleCell

Users that are interested in awesome-AI4SingleCell are comparing it to the libraries listed below

• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆98Updated 2 months ago
• jsxlei / SCALE
  Single-cell ATAC-seq analysis via Latent feature Extraction
  ☆103Updated 2 years ago
• jsxlei / SCALEX
  Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
  ☆79Updated last month
• Durenlab / LINGER
  ☆117Updated 5 months ago
• SONGDONGYUAN1994 / scDesign3
  scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
  ☆107Updated last month
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆111Updated last year
• JackieHanLab / TOSICA
  Transformer for One-Stop Interpretable Cell-type Annotation
  ☆144Updated last year
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆70Updated last year
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆152Updated 8 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆142Updated 2 years ago
• labomics / midas
  PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).
  ☆59Updated 2 months ago
• lanagarmire / Asgard
  ☆44Updated last year
• theislab / scib-reproducibility
  Additional code and analysis from the single-cell integration benchmarking project
  ☆67Updated 2 years ago
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆93Updated 2 months ago
• madilabcode / scNET
  ☆54Updated last month
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆152Updated last year
• ZJUFanLab / scDeepSort
  Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network
  ☆106Updated 2 years ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 4 years ago
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆91Updated last week
• gao-lab / Cell_BLAST
  A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
  ☆93Updated last year
• quadbio / scMultiome_analysis_vignette
  Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
  ☆68Updated last year
• YosefLab / popV
  ☆83Updated this week
• mossjacob / pyslingshot
  Python implementation of the Slingshot pseudotime algorithm
  ☆66Updated last week
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆114Updated this week
• pinellolab / simba
  SIMBA: SIngle-cell eMBedding Along with features
  ☆63Updated last year
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆122Updated last month
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆175Updated last year
• KrishnaswamyLab / SingleCellWorkshop
  ☆95Updated 4 years ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆121Updated this week
• jfnavarro / st_pipeline
  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …
  ☆88Updated 8 months ago