Alternatives and similar repositories for SpiceMix

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

• zcang / SpaOTsc
  ☆45Updated 2 years ago
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆110Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆68Updated 3 months ago
• theislab / scib-reproducibility
  Additional code and analysis from the single-cell integration benchmarking project
  ☆65Updated 2 years ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 7 months ago
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆59Updated this week
• scverse / scvi-tutorials
  Notebooks used in scvi-tools tutorials
  ☆52Updated this week
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated last month
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated last year
• raphael-group / paste
  Probabilistic Alignment of Spatial Transcriptomics Experiments
  ☆87Updated 3 months ago
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆107Updated 8 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆73Updated 4 months ago
• Lotfollahi-lab / nichecompass
  End-to-end analysis of spatial multi-omics data
  ☆75Updated 2 months ago
• bowang-lab / DeepVelo
  ☆47Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆60Updated 11 months ago
• wukevin / babel
  Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
  ☆42Updated last year
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆69Updated last year
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆42Updated 3 years ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆117Updated 9 months ago
• ZJUFanLab / SpaTalk
  Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data
  ☆71Updated 4 months ago
• rajewsky-lab / novosparc
  ☆130Updated last year
• Teichlab / bbknn
  Batch balanced KNN
  ☆161Updated last year
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆49Updated 10 months ago
• shuxiaoc / mario-py
  MARIO: single-cell proteomic data matching and integration using both shared and distinct features
  ☆23Updated last year
• cantinilab / scPRINT
  single cell foundation model for Gene network inference and more
  ☆81Updated this week
• gifford-lab / prescient
  Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
  ☆47Updated 4 months ago
• mossjacob / pyslingshot
  Python implementation of the Slingshot pseudotime algorithm
  ☆61Updated last year
• lilab-bcb / harmony-pytorch
  ☆54Updated last week
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆101Updated last year
• ZhangLabGT / scMultiSim
  A simulator for single cell multi-omics and spatial omics data that provides ground truth to benchmark a wide range of methods.
  ☆47Updated 4 months ago