Alternatives and similar repositories for singleCellHaystack:

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

• MarioniLab / DropletUtils
  Clone of the Bioconductor repository for the DropletUtils package.
  ☆57Updated 4 months ago
• elimereu / matchSCore2
  ☆55Updated 4 years ago
• morris-lab / Capybara
  Capybara: A computational tool to measure cell identity and fate transitions
  ☆58Updated 2 years ago
• RausellLab / CelliD
  Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
  ☆94Updated last year
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆77Updated 8 months ago
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆94Updated 3 years ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆49Updated 4 years ago
• andygxzeng / BoneMarrowMap
  A single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic …
  ☆48Updated last week
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆110Updated last week
• niaid / dsb
  Normalize CITEseq Data
  ☆65Updated last month
• abelson-lab / scATOMIC
  Pan-Cancer Single Cell Classifier
  ☆68Updated 11 months ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆76Updated last year
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆62Updated last year
• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆51Updated last year
• lhe17 / nebula
  ☆41Updated last month
• pachterlab / voyager
  From geospatial to spatial -omics
  ☆90Updated last month
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆76Updated 2 years ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆60Updated 2 years ago
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆95Updated 4 years ago
• mojaveazure / loomR
  An R-based interface for loom files
  ☆66Updated 4 years ago
• MarioniLab / miloDE
  Framework for sensitive DE testing (using neighbourhoods)
  ☆66Updated 9 months ago
• single-cell-genetics / vireo
  Demultiplexing pooled scRNA-seq data with or without genotype reference
  ☆83Updated 3 weeks ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆73Updated 8 months ago
• MarioniLab / scran
  Clone of the Bioconductor repository for the scran package.
  ☆41Updated 8 months ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆81Updated last month
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆44Updated 4 years ago
• EDePasquale / DoubletDecon
  A tool for removing doublets from single-cell RNA-seq data
  ☆73Updated 4 years ago
• stemangiola / CuratedAtlasQueryR
  Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
  ☆90Updated 4 months ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 2 weeks ago
• jon-xu / scSplit
  Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples withi…
  ☆41Updated 2 years ago