Alternatives and similar repositories for NICHES

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

• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆75Updated last year
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆32Updated last year
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆73Updated last month
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆61Updated last year
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆79Updated 2 years ago
• aet21 / SCENT
  Estimation of Single-Cell Potency with Single Cell Entropy
  ☆42Updated 2 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆104Updated last year
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆88Updated last month
• Banovich-Lab / Spatial_PF
  ☆31Updated last month
• KlugerLab / DAseq
  ☆41Updated 4 years ago
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆29Updated 9 months ago
• ShellyCoder / cellcall
  inferring cell-cell communication from scRNA-seq of ligand-receptor
  ☆84Updated last year
• ccruizm / GBmap
  Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolu…
  ☆61Updated 2 years ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 2 months ago
• Winnie09 / Lamian
  ☆56Updated 3 weeks ago
• zhengrongbin / MEBOCOST
  A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data
  ☆78Updated last month
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆88Updated 2 months 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 4 years ago
• jumphone / Vector
  Unsupervised Inference of Developmental Directions for Single Cells
  ☆22Updated last year
• Sanofi-Public / enact-pipeline
  Repository for ENACT pipeline for end-to-end analysis of Visium HD data
  ☆62Updated 3 months ago
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆87Updated 8 months ago
• FloWuenne / scFunctions
  Functions for single cell data analysis
  ☆32Updated 4 years ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆64Updated last week
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆80Updated 3 years ago
• YingMa0107 / IRIS
  Integrative and Reference-Informed Spatial Domain Detection for Spatial Transcriptomics
  ☆37Updated 7 months ago
• axelalmet / flowsig
  Python package to find communication-driven intercellular flows from single-cell RNA-sequencing and spatial transcriptomics data.
  ☆77Updated 4 months ago
• linnarsson-lab / developing-human-brain
  ☆35Updated last year
• 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
• Yelab2020 / Cottrazm
  Construct Tumor Transition Zone Microenvironment
  ☆48Updated 2 months ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆87Updated 3 months ago