Alternatives and similar repositories for immunedeconv

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

• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆540Updated this week
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆468Updated 2 months ago
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆500Updated last year
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆297Updated 4 years ago
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆614Updated 4 months ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆333Updated this week
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆333Updated 6 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆413Updated 3 weeks ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆286Updated 2 weeks ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆421Updated 3 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆425Updated last year
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆318Updated 2 years ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆324Updated this week
• IanevskiAleksandr / sc-type
  ☆265Updated 6 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆404Updated last month
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆296Updated 3 months ago
• cole-trapnell-lab / monocle3
  ☆386Updated this week
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆214Updated last month
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆409Updated 2 months ago
• Teichlab / cellphonedb
  ☆355Updated 3 years ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆573Updated 6 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆465Updated 2 weeks ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆374Updated 4 months ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆505Updated last year
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆306Updated 2 years ago
• quadbio / scRNAseq_analysis_vignette
  Tutorial for scRNA-seq data analysis beginners using R
  ☆199Updated 2 months ago
• hbctraining / DGE_workshop
  ☆392Updated 3 years ago
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆451Updated last year
• navinlabcode / copykat
  ☆235Updated 11 months ago
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆379Updated 6 months ago