Alternatives and similar repositories for SpiceMix

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

• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆111Updated last year
• zcang / SpaOTsc
  ☆45Updated 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
  ☆60Updated last week
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆107Updated 8 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆71Updated 4 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆63Updated last year
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆43Updated 3 years ago
• bowang-lab / DeepVelo
  ☆47Updated last year
• theislab / scib-reproducibility
  Additional code and analysis from the single-cell integration benchmarking project
  ☆67Updated 2 years ago
• ZJUFanLab / SpaTalk
  Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data
  ☆71Updated 5 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆60Updated last year
• wukevin / babel
  Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
  ☆42Updated last year
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆118Updated 9 months ago
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆69Updated last year
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated 2 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆73Updated 5 months ago
• rajewsky-lab / novosparc
  ☆130Updated last year
• gifford-lab / prescient
  Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
  ☆48Updated 5 months ago
• LungCellAtlas / HLCA_reproducibility
  This repository contains all code used for the Human Lung Cell Atlas project.
  ☆49Updated last year
• theislab / graphcompass
  GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
  ☆34Updated 2 months ago
• YosefLab / velovi
  ☆40Updated last week
• YangLabHKUST / Portal
  Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets
  ☆30Updated last year
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆68Updated this week
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆78Updated 6 months ago
• shuxiaoc / mario-py
  MARIO: single-cell proteomic data matching and integration using both shared and distinct features
  ☆22Updated last year
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆50Updated 11 months ago
• welch-lab / pyliger
  Python package for integrating and analyzing multiple single-cell datasets (A Python version of LIGER)
  ☆30Updated last month
• SONGDONGYUAN1994 / scDesign3
  scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
  ☆97Updated 3 months ago
• raphael-group / paste
  Probabilistic Alignment of Spatial Transcriptomics Experiments
  ☆88Updated 3 months ago