Alternatives and similar repositories for SpotClean

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

• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆73Updated 9 months ago
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆55Updated 3 months ago
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆61Updated last year
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆87Updated last month
• KlugerLab / DAseq
  ☆41Updated 4 years ago
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆46Updated last year
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆85Updated 2 months ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆75Updated 11 months ago
• califano-lab / single-cell-pipeline
  ☆50Updated 5 years ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆79Updated 4 months ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆23Updated last month
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆28Updated 8 months ago
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆74Updated 2 years ago
• RausellLab / CelliD
  Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
  ☆95Updated last year
• califano-lab / PISCES
  R package for Protein activity analysis of single-cell RNAseq.
  ☆83Updated 2 years ago
• FloWuenne / scFunctions
  Functions for single cell data analysis
  ☆32Updated 4 years ago
• TiedemannLab / sciCNV
  Dissecting the effects of DNA copy number variations on transcriptional programs at single-cell resolution
  ☆13Updated 3 years ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆86Updated 2 months ago
• veltenlab / CloneTracer
  This repository contains scripts to identify healthy and malignant cells from scRNAseq with CloneTracer and process data from Optimized 1…
  ☆26Updated 9 months ago
• ccruizm / GBmap
  Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolu…
  ☆58Updated 2 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆103Updated 10 months ago
• snehamitra / SCARlink
  ☆55Updated last month
• harbourlab / uphyloplot2
  Draw phylogenetic trees of tumor evolution
  ☆81Updated 2 years ago
• spcdot / CopyscAT
  Inferring CNV data from single cell ATAC seq
  ☆24Updated last month
• campbio / decontX
  Methods for decontamination of single cell data
  ☆47Updated 5 months ago
• Winnie09 / Lamian
  ☆55Updated last year
• haniffalab / scRNA-seq_analysis
  Single cell RNA-seq analysis bundle
  ☆35Updated 5 years ago
• buenrostrolab / stimATAC_analyses_code
  All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs
  ☆41Updated 2 years ago
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆40Updated last month
• dpeerlab / pdac-progression
  ☆10Updated 2 years ago