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
  ☆374Updated 5 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆412Updated last week
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆276Updated 2 years ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆419Updated 2 months ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆189Updated 3 months ago
• navinlabcode / copykat
  ☆233Updated 10 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.
  ☆253Updated 3 weeks ago
• cole-trapnell-lab / monocle3
  ☆380Updated 4 months ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆273Updated this week
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆422Updated last year
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆536Updated this week
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆332Updated last week
• IanevskiAleksandr / sc-type
  ☆262Updated 6 months ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆331Updated 5 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆326Updated 9 months ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆295Updated 4 years ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆281Updated 2 years ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆464Updated last month
• Teichlab / cellphonedb
  ☆355Updated 3 years ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆486Updated last week
• Danko-Lab / BayesPrism
  A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
  ☆184Updated 5 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆283Updated this week
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆323Updated this week
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆212Updated last month
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆227Updated 2 years ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆224Updated 2 weeks ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆317Updated 2 years ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆339Updated 2 months ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆363Updated 11 months ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆369Updated 4 months ago