Alternatives and similar repositories for SCENICprotocol

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

• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆150Updated 3 years ago
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆199Updated last month
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆140Updated 4 years ago
• neurorestore / Libra
  ☆180Updated 7 months ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆235Updated 2 years ago
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆240Updated 11 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆175Updated 4 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆184Updated 2 years ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆226Updated last year
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆138Updated 2 years ago
• mdozmorov / scATAC-seq_notes
  scATAC-seq data analysis tools and papers
  ☆126Updated 5 months ago
• sunduanchen / Scissor
  Scissor package
  ☆243Updated last year
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆169Updated last year
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆226Updated last year
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆122Updated last year
• digitalcytometry / cytotrace2
  CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.
  ☆206Updated last month
• wu-yc / scMetabolism
  Quantifying metabolism activity at the single-cell resolution
  ☆149Updated 5 months ago
• 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
  ☆122Updated 2 years ago
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆194Updated last week
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆179Updated last year
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆215Updated last year
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆160Updated 4 years ago
• YosefLab / Compass
  In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
  ☆119Updated last month
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆189Updated 3 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆174Updated 8 months ago
• navinlabcode / copykat
  ☆259Updated 2 months ago
• neurorestore / Augur
  Cell type prioritization in single-cell data
  ☆131Updated last year
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆302Updated 3 years ago
• carmonalab / UCell
  Gene set scoring for single-cell data
  ☆174Updated last month
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆222Updated last week