Alternatives and similar repositories for seurat:

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

• theislab / single-cell-tutorial
  Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…
  ☆1,472Updated 2 years ago
• YuLab-SMU / clusterProfiler
  A universal enrichment tool for interpreting omics data
  ☆1,088Updated last week
• sqjin / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
  ☆690Updated last year
• seandavi / awesome-single-cell
  Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
  ☆3,355Updated this week
• hemberg-lab / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆674Updated 3 years ago
• hbctraining / scRNA-seq
  ☆556Updated 4 years ago
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆889Updated this week
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆692Updated last week
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆606Updated 2 months ago
• cole-trapnell-lab / monocle3
  ☆379Updated 3 months ago
• scverse / scanpy
  Single-cell analysis in Python. Scales to >100M cells.
  ☆2,075Updated this week
• hbctraining / Intro-to-scRNAseq
  ☆579Updated last week
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆565Updated 5 months ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆460Updated last month
• mikelove / awesome-multi-omics
  List of software packages for multi-omics analysis
  ☆778Updated last week
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆790Updated 8 months ago
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆1,002Updated 3 years ago
• crazyhottommy / scRNAseq-analysis-notes
  scRNAseq analysis notes from Ming Tang
  ☆693Updated 4 months ago
• Starlitnightly / omicverse
  A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
  ☆605Updated last week
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆482Updated 11 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆391Updated last week
• crazyhottommy / getting-started-with-genomics-tools-and-resources
  Unix, R and python tools for genomics and data science
  ☆1,267Updated last month
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,016Updated this week
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆364Updated 3 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆534Updated 2 weeks ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆483Updated 2 weeks ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆330Updated 5 months ago
• kpatel427 / YouTubeTutorials
  ☆315Updated 6 months ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆497Updated last year
• griffithlab / rnaseq_tutorial
  Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis inclu…
  ☆1,365Updated last year