Alternatives and similar repositories for scAI

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

• KlugerLab / ALRA
  Imputation method for scRNA-seq based on low-rank approximation
  ☆77Updated last year
• zhengtaoxiao / Single-Cell-Metabolic-Landscape
  Pipeline for characterizing metebolic heterogeneity from single-cell RNA-seq data
  ☆22Updated 3 years ago
• Teichlab / Pan_fetal_immune
  Collection of scripts for analysis of pan fetal immune atlas
  ☆27Updated 3 years ago
• forrest-lab / NATMI
  NATMI: Network Analysis Toolkit for the Multicellular Interactions
  ☆35Updated 4 years ago
• wycwycpku / RSCORE
  ☆26Updated 3 years ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆63Updated last month
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 2 years ago
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆46Updated last year
• cssmillie / ulcerative_colitis
  ☆63Updated 4 years ago
• sankaranlab / SCAVENGE
  SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.
  ☆87Updated last year
• LungCellAtlas / HLCA_reproducibility
  This repository contains all code used for the Human Lung Cell Atlas project.
  ☆51Updated 2 years ago
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆84Updated 8 months ago
• edsgard / trendsceek
  Identify genes with spatial expression trends in single-cell gene expression data
  ☆50Updated 7 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆104Updated 11 months ago
• Single-Cell-Genomics-Group-CNAG-CRG / Tumor-Immune-Cell-Atlas
  Code repository for the Tumor Immune Cell Atlas (TICA) project
  ☆64Updated 3 years ago
• tanlabcode / CytoTalk
  A novel computational method for inferring cell-type-specific signaling networks using single-cell transcriptomics data for better charac…
  ☆43Updated 11 months ago
• haniffalab / FCA_liver
  All software used for “Decoding human fetal liver haematopoiesis” (Popescu, Botting, Stephenson et al., 2019).
  ☆39Updated 5 years ago
• scCOVID-19 / COVIDPBMC
  Multi-omics profiling of peripheral immune system response to SARS-CoV-2 infection
  ☆41Updated 3 years ago
• quadbio / scMultiome_analysis_vignette
  Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
  ☆64Updated last year
• CostaLab / scMEGA
  scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
  ☆40Updated 11 months ago
• vibscc / DALI
  R-package for the analysis of single-cell TCR/BCR data in the Seurat ecosystem
  ☆20Updated 4 months ago
• LungCellAtlas / scRNAseq_pipelines
  Repository for the building, sharing and editing of scRNAseq pipelines for the Lung Cell Atlas
  ☆38Updated 4 years ago
• dtsoucas / DWLS
  Gene expression deconvolution using dampened weighted least squares
  ☆29Updated 4 years ago
• bioinfoDZ / RISC
  A R package for integrated scRNA-seq data analysis using the RPCI algorithm
  ☆44Updated last year
• morris-lab / BiddyetalWorkflow
  This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.
  ☆32Updated last year
• cellgeni / batchbench
  ☆47Updated 3 years ago
• morris-lab / Capybara
  Capybara: A computational tool to measure cell identity and fate transitions
  ☆59Updated 3 years ago
• cailab-tamu / scTenifoldKnk
  R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.
  ☆61Updated 7 months ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 2 years ago
• matanhofree / crc-immune-hubs
  Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organiz…
  ☆38Updated 3 years ago