Alternatives and similar repositories for scaden

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

• favilaco / deconv_benchmark
  ☆58Updated 5 years ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆79Updated 9 months ago
• cellgeni / batchbench
  ☆46Updated 3 years ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆153Updated last year
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆106Updated 2 years ago
• gao-lab / Cell_BLAST
  A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
  ☆94Updated last year
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆122Updated last month
• immunogenomics / LISI
  Methods to compute Local Inverse Simpson's Index (LISI)
  ☆70Updated 4 years ago
• SpatialTranscriptomicsResearch / st_pipeline
  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …
  ☆84Updated 4 years ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆144Updated 2 years ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆66Updated 4 months ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆77Updated 2 months ago
• rajewsky-lab / novosparc
  ☆131Updated 2 years ago
• mohuangx / SAVER
  Single-cell RNA-seq Gene Expression Recovery
  ☆111Updated 11 months ago
• KrishnaswamyLab / SingleCellWorkshop
  ☆96Updated 4 years ago
• dtsoucas / DWLS
  Gene expression deconvolution using dampened weighted least squares
  ☆31Updated 4 years ago
• calico / solo
  software to detect doublets
  ☆95Updated 10 months ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆93Updated last month
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆114Updated last year
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆139Updated 2 years ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆159Updated 2 weeks ago
• JinmiaoChenLab / Batch-effect-removal-benchmarking
  A benchmark of batch-effect correction methods for single-cell RNA sequencing data
  ☆79Updated 3 years ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆142Updated last week
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆97Updated 6 years ago
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆92Updated 3 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated 2 weeks ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆46Updated 4 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆105Updated last year
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆111Updated 2 years ago
• Durenlab / LINGER
  ☆119Updated 5 months ago