Alternatives and similar repositories for infercnv

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

• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆477Updated 3 months ago
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆509Updated last year
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆548Updated 2 weeks ago
• cole-trapnell-lab / monocle3
  ☆388Updated 2 weeks ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆334Updated 7 months ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆423Updated 4 months ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆375Updated 5 months ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆325Updated this week
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆468Updated last month
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆420Updated 2 months ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆577Updated 7 months ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆413Updated 3 weeks ago
• Teichlab / cellphonedb
  ☆355Updated 3 years ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆298Updated 4 years ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆336Updated this week
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆318Updated 2 years ago
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆307Updated 2 years ago
• hbctraining / Intro-to-scRNAseq
  ☆601Updated 2 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆495Updated last month
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆416Updated last month
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆394Updated 2 weeks ago
• hbctraining / DGE_workshop
  ☆392Updated 3 years ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆422Updated 11 months ago
• hbctraining / Intro-to-DGE
  ☆199Updated 3 months ago
• junjunlab / scRNAtoolVis
  Useful functions to make your scRNA-seq plot more cool!
  ☆344Updated last month
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆703Updated 2 weeks ago
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆456Updated last year
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆428Updated last year
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆805Updated 10 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆288Updated this week