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
  ☆107Updated 2 years ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆89Updated last year
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆95Updated 2 years ago
• ShobiStassen / VIA
  trajectory inference
  ☆104Updated 5 months ago
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆115Updated 2 months ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆150Updated last month
• bioinfo-ibms-pumc / SCSA
  SCSA: cell type annotation for single-cell RNA-seq data
  ☆90Updated 2 years ago
• liulab-dfci / RIMA_pipeline
  ☆82Updated last year
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 2 months ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆117Updated this week
• rpolicastro / scProportionTest
  ☆68Updated last year
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆105Updated 2 years ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆110Updated 2 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆77Updated 3 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆74Updated 5 months ago
• KChen-lab / METAFlux
  ☆68Updated last year
• BostonGene / Kassandra
  Bostongene cell deconvolution algorithm from RNAseq
  ☆55Updated last year
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated 2 years ago
• satijalab / azimuth
  A Shiny web app for mapping datasets using Seurat v4
  ☆132Updated 8 months ago
• YosefLab / popV
  ☆79Updated last week
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆68Updated 5 years ago
• AllonKleinLab / SPRING_dev
  ☆69Updated last year
• omnideconv / omnideconv
  Unified access to several second-generation deconvolution methods
  ☆73Updated this week
• RausellLab / CelliD
  Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
  ☆95Updated last year
• cellgeni / STARsolo
  wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
  ☆60Updated last month
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆101Updated 10 months ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆63Updated last year
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆103Updated last year
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆108Updated 3 months ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆149Updated last year