Alternatives and similar repositories for concordex

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

• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆61Updated 2 months ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆42Updated 5 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆44Updated 3 weeks ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated last week
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆55Updated 4 months ago
• nf-core / spatialxe
  ☆22Updated this week
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆35Updated 3 weeks ago
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆65Updated 3 months ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆38Updated 4 months ago
• const-ae / pyLemur
  A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
  ☆26Updated 9 months ago
• wanglab-broad / CAST
  CAST package
  ☆40Updated 11 months ago
• scverse / ecosystem-packages
  Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
  ☆29Updated this week
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆66Updated 3 weeks ago
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆16Updated last month
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆31Updated 2 weeks ago
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆29Updated last year
• Teichlab / sctk
  ☆41Updated 2 months ago
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆81Updated 3 years ago
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆55Updated last year
• rajewsky-lab / spacemake
  ☆45Updated 2 weeks ago
• JEFworks-Lab / veloviz
  RNA-velocity informed embeddings for visualizing cellular trajectories
  ☆45Updated 3 years ago
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆31Updated this week
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 8 months ago
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆39Updated 7 months ago
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆27Updated last year
• immunitastx / monkeybread
  Analyzing cellular niches in spatial transcriptomics data
  ☆31Updated 11 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆84Updated 3 months ago
• almaan / eggplant
  ☆22Updated 3 years ago
• JCVenterInstitute / NSForest
  A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…
  ☆65Updated 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 3 years ago