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
  ☆558Updated last week
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆340Updated 8 months ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆343Updated this week
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆291Updated 2 weeks ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆483Updated 4 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆417Updated last week
• cole-trapnell-lab / monocle3
  ☆396Updated last month
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆424Updated 5 months ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆300Updated 5 years ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆434Updated last year
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆630Updated 6 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆438Updated last month
• IanevskiAleksandr / sc-type
  ☆271Updated 8 months ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆423Updated 3 weeks ago
• Teichlab / cellphonedb
  ☆356Updated 3 years ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆328Updated this week
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆586Updated 8 months ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆383Updated 2 weeks ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆527Updated last month
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆220Updated 3 months ago
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆536Updated last year
• alserglab / fgsea
  Fast Gene Set Enrichment Analysis
  ☆409Updated 3 weeks ago
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆463Updated last year
• cole-trapnell-lab / monocle-release
  ☆289Updated 3 years ago
• BioinformaticsFMRP / TCGAbiolinks
  TCGAbiolinks
  ☆328Updated last month
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆318Updated 2 years ago
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆261Updated 8 months ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆355Updated 5 months ago
• hbctraining / Intro-to-scRNAseq
  ☆611Updated 3 months ago
• NBISweden / excelerate-scRNAseq
  Single RNA-seq data analysis with R (Finland, May, 2019)
  ☆226Updated 3 years ago