Alternatives and similar repositories for scJoint

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

• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆47Updated 4 years ago
• theislab / scib-reproducibility
  Additional code and analysis from the single-cell integration benchmarking project
  ☆71Updated 3 years ago
• YangLabHKUST / Portal
  Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets
  ☆33Updated 2 years ago
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆71Updated 2 years ago
• navinlabcode / CellTrek
  ☆126Updated 3 years ago
• jsxlei / SCALEX
  Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
  ☆79Updated 3 months ago
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆62Updated 3 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆66Updated 5 months ago
• raphael-group / paste
  Probabilistic Alignment of Spatial Transcriptomics Experiments
  ☆98Updated 9 months ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆137Updated 10 months ago
• theislab / regvelo
  inferring regulatory cellular dynamics
  ☆61Updated 3 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆126Updated last month
• kunwang34 / PhyloVelo
  PhyloVelo, Phylogeny-based transcriptomic velocity of single cells
  ☆43Updated 3 months ago
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆116Updated last year
• immunogenomics / LISI
  Methods to compute Local Inverse Simpson's Index (LISI)
  ☆72Updated 4 years ago
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆116Updated last year
• SONGDONGYUAN1994 / scDesign3
  scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
  ☆111Updated 2 months ago
• snehamitra / SCARlink
  ☆61Updated 2 weeks ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆77Updated 10 months ago
• 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 2 weeks ago
• tabdelaal / SpaGE
  Enhancing spatial transcriptomics data by predicting the expression of unmeasured genes from a dissociated scRNA-seq data
  ☆40Updated last year
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆78Updated this week
• Durenlab / LINGER
  ☆119Updated 6 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆80Updated 11 months ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆113Updated last year
• yunguan-wang / SPROD
  SPROD: Spatial expression profiling de-noising
  ☆36Updated 2 years ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last month
• zhanglhbioinfor / DIRECT-NET
  ☆12Updated 2 years ago
• quadbio / scMultiome_analysis_vignette
  Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
  ☆68Updated last year
• drieslab / spatial-datasets
  overview of spatial datasets
  ☆76Updated last year