Alternatives and similar repositories for SpotClean

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

• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆58Updated this week
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆80Updated 5 months ago
• califano-lab / single-cell-pipeline
  ☆50Updated 6 years ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆97Updated 8 months ago
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆88Updated 3 years ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆77Updated last year
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆92Updated last month
• jlaffy / infercna
  Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data
  ☆46Updated 2 years ago
• RausellLab / CelliD
  Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
  ☆95Updated 2 years ago
• KlugerLab / DAseq
  ☆41Updated 4 years ago
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆29Updated last year
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆62Updated last year
• harbourlab / uphyloplot2
  Draw phylogenetic trees of tumor evolution
  ☆87Updated 2 years ago
• califano-lab / PISCES
  R package for Protein activity analysis of single-cell RNAseq.
  ☆87Updated 3 years ago
• jumphone / Vector
  Unsupervised Inference of Developmental Directions for Single Cells
  ☆23Updated 2 years ago
• Winnie09 / Lamian
  ☆61Updated 5 months ago
• ccruizm / GBmap
  Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolu…
  ☆65Updated 3 years ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆84Updated 10 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆106Updated last year
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆95Updated last week
• FloWuenne / scFunctions
  Functions for single cell data analysis
  ☆32Updated 4 years ago
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆46Updated 5 months ago
• campbio / decontX
  Methods for decontamination of single cell data
  ☆56Updated 11 months ago
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆51Updated last year
• veltenlab / CloneTracer
  This repository contains scripts to identify healthy and malignant cells from scRNAseq with CloneTracer and process data from Optimized 1…
  ☆26Updated last year
• hernet / transcriptional-map-nk
  We describe a transcriptional reference map of human natural killer (NK) cells based on analysis of scRNA-seq data from both blood and ti…
  ☆14Updated last year
• bioinfoDZ / RISC
  A R package for integrated scRNA-seq data analysis using the RPCI algorithm
  ☆44Updated last year
• Coolgenome / iTALK
  ☆65Updated 6 years ago
• aet21 / SCENT
  Estimation of Single-Cell Potency with Single Cell Entropy
  ☆43Updated 2 years ago
• arc85 / celltalker
  Inference of cell-cell communication from single-cell RNAseq data
  ☆49Updated 9 months ago