Alternatives and similar repositories for omicverse

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

• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆453Updated last year
• Starlitnightly / single_cell_tutorial
  单细胞分析的中文pipeline
  ☆263Updated last year
• hbctraining / scRNA-seq
  ☆591Updated 4 years ago
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆759Updated last week
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆598Updated last week
• hbctraining / Intro-to-scRNAseq
  ☆635Updated this week
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆564Updated 5 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆497Updated 2 months ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆447Updated 6 months ago
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆1,072Updated 3 weeks ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆401Updated 10 months ago
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆677Updated 2 weeks ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆596Updated 3 weeks ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆433Updated last week
• genecell / single-cell-papers-with-code
  Papers with code for single cell related papers
  ☆299Updated 2 years ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆448Updated last year
• 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…
  ☆1,532Updated 2 years ago
• gao-lab / Guideline-for-Computational-Biology-and-Bioinformatics
  ☆368Updated 7 months ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆477Updated 3 weeks ago
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆469Updated last year
• jmzeng1314 / GEO
  ☆855Updated 3 years ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆396Updated 3 weeks ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆512Updated last month
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆647Updated 3 weeks ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆511Updated 8 months ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆393Updated 3 months ago
• hemberg-lab / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆675Updated 3 years ago
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆267Updated last week
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆330Updated 9 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆486Updated 6 months ago