Alternatives and similar repositories for hdWGCNA:

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

• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆362Updated 4 months ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆268Updated 2 years ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆328Updated 4 months 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.
  ☆247Updated last week
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆416Updated last year
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆185Updated last month
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆328Updated last week
• cole-trapnell-lab / monocle3
  ☆375Updated 2 months ago
• IanevskiAleksandr / sc-type
  ☆257Updated 4 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆526Updated last month
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆292Updated 4 years ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆221Updated 3 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆407Updated 2 months ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆408Updated last month
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆268Updated last month
• navinlabcode / copykat
  ☆228Updated 9 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆318Updated 8 months ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆452Updated 2 weeks ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆278Updated 2 years ago
• NBISweden / excelerate-scRNAseq
  Single RNA-seq data analysis with R (Finland, May, 2019)
  ☆221Updated 2 years ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆226Updated last year
• immunogenomics / presto
  Fast Wilcoxon and auROC
  ☆176Updated 4 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆272Updated 6 months ago
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆469Updated 10 months ago
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆280Updated last month
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆314Updated last year
• statOmics / tradeSeq
  TRAjectory-based Differential Expression analysis for SEQuencing data
  ☆251Updated 2 months ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆377Updated 2 months ago
• saezlab / decoupleR
  R package to infer biological activities from omics data using a collection of methods.
  ☆234Updated 3 weeks ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆349Updated last week