Alternatives and similar repositories for NicheDE:

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

• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆26Updated 3 months ago
• MarioniLab / StabMap
  Mosaic single cell data integration using non-overlapping features
  ☆37Updated 2 years ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆31Updated 2 weeks ago
• KlugerLab / DAseq
  ☆39Updated 3 years ago
• ZJUFanLab / CellTalkDB
  A manually curated database of literature-supported ligand-receptor interactions in human and mouse
  ☆29Updated 8 months ago
• atakanekiz / CIPR-Package
  Cluster Identity Predictor (R package implementation)
  ☆20Updated 3 years ago
• hsmaan / Iniquitate
  Analysis of imbalanced data and its impacts in a scRNA-seq integration setting
  ☆30Updated this week
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆31Updated 9 months ago
• JinmiaoChenLab / FastIntegration
  FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis
  ☆23Updated 4 months ago
• saezlab / MOFAcellulaR
  R package to infer multicellular programs from single-cell data using multi-omics factor analysis (MOFA)
  ☆8Updated last year
• rikenbit / scTensor
  R package for detection of cell-cell interaction using Non-negative Tensor Decomposition
  ☆34Updated 2 years ago
• omnideconv / spacedeconv
  A unified interface to spatial transcriptomics deconvolution tools
  ☆40Updated last week
• yunguan-wang / Spacia
  ☆27Updated 4 months ago
• greenelab / miQC
  Flexible, probablistic metrics for quality control of scRNA-seq data
  ☆19Updated 2 years ago
• saeyslab / spotless-benchmark
  A repository for benchmarking spatial deconvolution and mapping tools
  ☆32Updated last month
• Winnie09 / Lamian
  ☆50Updated 7 months ago
• CamaraLab / ConDecon
  R package: ConDecon is a clustering-independent deconvolution method for estimating cell abundances in bulk tissues using single-cell RNA…
  ☆12Updated 4 months ago
• Teichlab / HCA_Heart_ver2
  ☆28Updated last year
• cbib / Seurat-Integrate
  R package gathering a set of wrappers to apply various integration methods to Seurat objects (and rate such methods)
  ☆16Updated last month
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆60Updated 4 months ago
• Jiaxin-Fan / MuSiC2
  cell type deconvolution for multi-condition bulk RNA-seq data
  ☆23Updated 3 years ago
• LungCellAtlas / scRNAseq_pipelines
  Repository for the building, sharing and editing of scRNAseq pipelines for the Lung Cell Atlas
  ☆33Updated 4 years ago
• seasoncloud / Clonalscope
  Clonalscope is a subclone detection method based on copy number alterations (CNAs) for single-cell and ST tumor sequencing data. Clonalsc…
  ☆13Updated 5 months ago
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆33Updated 3 weeks ago
• azizilab / DIISCO_public
  Publically accessible code for DIISCO method
  ☆10Updated 4 months ago
• Teichlab / sctk
  ☆35Updated 5 months ago
• dpeerlab / pdac-progression
  ☆10Updated last year
• PoolLab / generecovery
  ☆29Updated last year