Alternatives and similar repositories for SCENICprotocol

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

• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆139Updated 3 years ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆231Updated 2 years ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆145Updated 3 years ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆210Updated last year
• neurorestore / Libra
  ☆173Updated 3 months ago
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆182Updated 3 weeks ago
• sunduanchen / Scissor
  Scissor package
  ☆231Updated last year
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆128Updated last year
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆233Updated 7 months ago
• digitalcytometry / cytotrace2
  CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.
  ☆161Updated 4 months ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆167Updated last year
• Dragonmasterx87 / Interactive-3D-Plotting-in-Seurat-3.0.0
  This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data
  ☆121Updated 2 years ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆152Updated last week
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆212Updated 11 months ago
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆118Updated 11 months ago
• navinlabcode / copykat
  ☆247Updated last year
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆173Updated 2 years ago
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆164Updated last year
• mdozmorov / scATAC-seq_notes
  scATAC-seq data analysis tools and papers
  ☆116Updated last month
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆166Updated 4 months ago
• Danko-Lab / BayesPrism
  A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
  ☆201Updated 2 months ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆155Updated 4 years ago
• wu-yc / scMetabolism
  Quantifying metabolism activity at the single-cell resolution
  ☆137Updated last month
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆184Updated 2 months ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆213Updated last year
• chuiqin / irGSEA
  The integration of single cell rank-based gene set enrichment analysis
  ☆130Updated last month
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆188Updated 9 months ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆291Updated 2 years ago
• YosefLab / Compass
  In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
  ☆112Updated 7 months ago
• neurorestore / Augur
  Cell type prioritization in single-cell data
  ☆124Updated 10 months ago