Alternatives and similar repositories for nichenetr:

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

• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆439Updated last week
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆398Updated last week
• Teichlab / cellphonedb
  ☆353Updated 3 years ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆282Updated 4 years ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆320Updated 2 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆346Updated 2 months ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆325Updated this week
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆405Updated 11 months ago
• cole-trapnell-lab / monocle3
  ☆363Updated last month
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆438Updated 8 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆402Updated last month
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆310Updated last year
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆593Updated 2 weeks ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆313Updated this week
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆306Updated 6 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆448Updated 2 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆263Updated 4 months ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆263Updated 2 months ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆264Updated 2 years ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆335Updated 8 months ago
• IanevskiAleksandr / sc-type
  ☆253Updated 3 months ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆349Updated 3 weeks ago
• samuel-marsh / scCustomize
  R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
  ☆242Updated last week
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆375Updated 2 weeks ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆333Updated last month
• liulab-dfci / TRUST4
  TCR and BCR assembly from RNA-seq data
  ☆293Updated this week
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆362Updated last month
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆353Updated 2 months ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆547Updated 3 months ago
• cellgeni / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆129Updated 2 years ago