Alternatives and similar repositories for ShortCake

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

• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆106Updated 2 years ago
• timoast / sinto
  Tools for single-cell data processing
  ☆125Updated last year
• AllonKleinLab / SPRING_dev
  ☆69Updated last year
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆90Updated last year
• rpolicastro / scProportionTest
  ☆71Updated last year
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆120Updated 3 weeks ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆79Updated 4 months ago
• bioinfo-ibms-pumc / SCSA
  SCSA: cell type annotation for single-cell RNA-seq data
  ☆91Updated 2 years ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆95Updated 2 years ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆149Updated last year
• cellgeni / STARsolo
  wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
  ☆61Updated last month
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆120Updated last week
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated 2 years ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆64Updated last year
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 3 months ago
• saezlab / transcriptutorial
  This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
  ☆56Updated 2 years ago
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆69Updated 5 years ago
• abelson-lab / scATOMIC
  Pan-Cancer Single Cell Classifier
  ☆74Updated last year
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆155Updated this week
• cssmillie / ulcerative_colitis
  ☆63Updated 4 years ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆138Updated last year
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆95Updated 4 years ago
• omnideconv / omnideconv
  Unified access to several second-generation deconvolution methods
  ☆73Updated 3 weeks ago
• theislab / AutoGeneS
  ☆61Updated 4 years ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆70Updated last week
• ShobiStassen / VIA
  trajectory inference
  ☆104Updated 6 months ago
• alexisvdb / singleCellHaystack
  Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
  ☆84Updated 11 months ago
• liulab-dfci / RIMA_pipeline
  ☆84Updated last year
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆105Updated 2 years ago
• gillislab / MetaNeighbor
  A method to rapidly assess cell type identity using both functional and random gene sets
  ☆39Updated 6 months ago