Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

Package Usage: cran: Seurat

Tools for Single Cell Genomics
38 versions
Latest release: 6 months ago
61 dependent packages
46,528 downloads last month

View more package details: https://packages.ecosyste.ms/registries/cran.r-project.org/packages/Seurat

View more repository details: https://repos.ecosyste.ms/hosts/GitHub/repositories/satijalab%2Fseurat

Dependent Repos 510

BlishLab/scriabin
Analysis of cell-cell communication at single-cell resolution
  • * DESCRIPTION

Size: 8.35 MB - Last synced: 3 months ago - Pushed: 9 months ago

cnio-bu/beyondcell
Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.
  • >= 3.2.2 DESCRIPTION

Size: 143 MB - Last synced: 2 months ago - Pushed: 2 months ago

vibscc/DALI
R-package for the analysis of single-cell TCR/BCR data in the Seurat ecosystem
  • >= 4.0.0 DESCRIPTION

Size: 8.95 MB - Last synced: about 2 months ago - Pushed: about 1 year ago

ZJUFanLab/scDisProcema
  • * DESCRIPTION

Size: 3.15 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

xu-lab/CellRef
Guided construction of single cell reference
  • * DESCRIPTION

Size: 88 MB - Last synced: 11 months ago - Pushed: 11 months ago

connorhknight/IBRAP
single-cell RNA-sequencing integrative, benchmarking tool.
  • >= 4.0.3 DESCRIPTION

Size: 327 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

maehrlab/thymusatlastools2
A set of general purpose tools for single cell analysis. Upgrade of thymusatlastools, also available on our Github.
  • >= 2.0.0 DESCRIPTION

Size: 39.6 MB - Last synced: about 1 year ago - Pushed: over 2 years ago

SGDDNB/ShinyCell
Shiny Interactive Web Apps for Single-Cell Data
  • DESCRIPTION

Size: 28.8 MB - Last synced: 4 days ago - Pushed: 3 months ago

NWhitener/scrnabench
A package for metamorphic benchmarking of scRNA-seq data analysis methods
  • * DESCRIPTION

Size: 183 MB - Last synced: 7 months ago - Pushed: 7 months ago

rujinwang/EPIC
cEll tyPe enrIChment
  • * package/DESCRIPTION

Size: 131 MB - Last synced: 8 months ago - Pushed: over 1 year ago

Fuyt27/dscBLAST
dscBLAST: developmental single cell Basic Local Alignment Search Tool
  • * DESCRIPTION

Size: 193 MB - Last synced: 7 months ago - Pushed: 7 months ago

sunduanchen/Scissor
Scissor package
  • >= 3.2.0 DESCRIPTION
  • * DESCRIPTION

Size: 28.5 MB - Last synced: 6 months ago - Pushed: over 2 years ago

JohnMariani/scPlottingTools
Some Plotting Functions to Speed Up Figure and Slide Generation
  • * DESCRIPTION

Size: 13.7 KB - Last synced: 12 months ago - Pushed: 12 months ago

asifzubair/GIST
Guiding-Image Spatial Transcriptomics
  • * DESCRIPTION

Size: 9.95 MB - Last synced: 9 months ago - Pushed: over 2 years ago

Close-your-eyes/scexpr
tools for single cell rna seq analysis
  • * DESCRIPTION

Size: 564 KB - Last synced: about 1 month ago - Pushed: about 1 month ago

enblacar/SCpubr
Generate high quality, publication ready visualizations for single cell transcriptomics data.
  • * DESCRIPTION

Size: 87.6 MB - Last synced: 11 days ago - Pushed: 3 months ago

immunogenomics/harmony
Fast, sensitive and accurate integration of single-cell data with Harmony
  • >= 4.1.1 DESCRIPTION

Size: 51.7 MB - Last synced: 2 months ago - Pushed: 4 months ago

cole-trapnell-lab/monocle-release
  • * DESCRIPTION

Size: 207 MB - Last synced: 2 months ago - Pushed: almost 2 years ago

satijalab/seurat-wrappers
Community-provided extensions to Seurat
  • >= 3.0.1 DESCRIPTION

Size: 116 MB - Last synced: 2 days ago - Pushed: 2 days ago

kharchenkolab/gpsFISH
Optimization of gene panels for targeted spatial transcriptomics
  • >= 4.0.3 DESCRIPTION

Size: 26.3 MB - Last synced: 6 months ago - Pushed: about 1 year ago

omnideconv/SimBu
Simulate pseudo-bulk RNAseq samples from scRNAseq expression data
  • * DESCRIPTION

Size: 18.6 MB - Last synced: 9 days ago - Pushed: 11 days ago

carmonalab/ProjecTILs
Interpretation of cell states using reference single-cell maps
  • * DESCRIPTION

Size: 54.4 MB - Last synced: 18 days ago - Pushed: 19 days ago

efranz7/rrrSingleCellUtils Fork of kidcancerlab/rrrSingleCellUtils
Single cell analysis utility functions for the Ryan Roberts lab
  • * DESCRIPTION

Size: 2.17 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

lazappi/clustree
Visualise Clusterings at Different Resolutions
  • >= 2.3.0 DESCRIPTION

Size: 36.9 MB - Last synced: 8 days ago - Pushed: 6 months ago

cuhklinlab/RA3
RA3 method for integrative analysis of single cell ATAC sequence data.
  • * DESCRIPTION

Size: 28.5 MB - Last synced: about 1 year ago - Pushed: about 3 years ago

SunXQlab/stMLnet
stMLnet: Dissecting spatial and multilayer cell-cell communications with stMLnet
  • * DESCRIPTION

Size: 8.31 MB - Last synced: 22 days ago - Pushed: 23 days ago

welch-lab/liger
R package for integrating and analyzing multiple single-cell datasets
  • * DESCRIPTION

Size: 193 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

Oshlack/speckle
R package for specialised analysis of single cell data
  • * DESCRIPTION

Size: 20.4 MB - Last synced: about 2 months ago - Pushed: over 1 year ago

sulab-wmu/scPagwas
Obtain trait-relevant cell subpopulations by incorporating pathway activity transformed scRNA-seq data with GWAS data
  • * DESCRIPTION

Size: 992 MB - Last synced: 5 days ago - Pushed: 24 days ago

carmonalab/STACAS
R package for semi-supervised single-cell data integration
  • >= 4.0.0 DESCRIPTION

Size: 101 MB - Last synced: 3 months ago - Pushed: 4 months ago

hms-dbmi/dseqr
single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.
  • * DESCRIPTION

Size: 34.3 MB - Last synced: 4 days ago - Pushed: about 1 month ago

samuel-marsh/scCustomize
R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
  • >= 4.0.6 DESCRIPTION
  • >= 4.0.5 DESCRIPTION

Size: 276 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

bioFAM/MOFA2
Multi-Omics Factor Analysis
  • * DESCRIPTION

Size: 162 MB - Last synced: 9 days ago - Pushed: 4 months ago

nbroguiere/burgertools
Bundle of Useful scRNA-seq Gating Tools Extending seuRat
  • >= 4.0.1 DESCRIPTION

Size: 43.9 MB - Last synced: 5 months ago - Pushed: 5 months ago

altairwei/rhapsodykit
A Comprehensive Toolkit to Analyze Multi-Sample Multi-Condition Single-Cell Transcriptomics Data
  • >= 4.0.0 DESCRIPTION

Size: 334 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

prabhakarlab/DUBStepR
Correlation-Based Feature Selection for Single-Cell RNA Sequencing Data
  • * DESCRIPTION

Size: 10.7 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

CostaLab/sigurd
Using single cell genotype data, the cells are annotated and analysed.
  • * DESCRIPTION

Size: 4.37 MB - Last synced: 5 months ago - Pushed: 5 months ago

swaruplabUCI/ArchRtoSignac
An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)
  • >= 4.1.0 DESCRIPTION

Size: 284 KB - Last synced: 2 months ago - Pushed: 2 months ago

ucagenomix/isoswitch
  • * DESCRIPTION

Size: 3.52 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

HelenLindsay/AbNames
Standardize antibody names and match to genes
  • * DESCRIPTION

Size: 42.1 MB - Last synced: 12 months ago - Pushed: 12 months ago

rseng/rsepedia-analysis
Exploring clustering of research software encyclopedia entries
  • >= 3.2.2 _repos/github/constantAmateur/SoupX/DESCRIPTION

Size: 435 MB - Last synced: 2 days ago - Pushed: 3 days ago

lima1/sttkit
Pipeline for SpatialTranscriptomics and 10X Visium data
  • >= 3.0.0 DESCRIPTION

Size: 541 KB - Last synced: 6 days ago - Pushed: 6 days ago

dtm2451/dittoSeq
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
  • >= 2.2 DESCRIPTION

Size: 18.7 MB - Last synced: 17 days ago - Pushed: 17 days ago

Nanostring-Biostats/GeomxTools
Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.
  • * DESCRIPTION

Size: 82.9 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

cellgeni/sceasy
A package to help convert different single-cell data formats to each other
  • >= 3.0.1 DESCRIPTION

Size: 74.2 KB - Last synced: 30 days ago - Pushed: 3 months ago

OscarGVelasco/ClusterFoldSimilarity
Calculate cluster similarity between clusters from different single cell datasets/batches/samples.
  • * DESCRIPTION

Size: 17.6 MB - Last synced: 10 days ago - Pushed: 11 days ago

drostlab/myTAI
Evolutionary Transcriptomics with R
  • * DESCRIPTION

Size: 71.9 MB - Last synced: 13 days ago - Pushed: about 1 month ago

RuiyuRayWang/scWidgets
A collection of scRNAseq functions re-written for easy analysis using the Seurat objects
  • * DESCRIPTION

Size: 41 KB - Last synced: 10 months ago - Pushed: over 2 years ago

jspaezp/sctree
Tree based marker finding and gating visualization for single cell rna seq data
  • * DESCRIPTION

Size: 38 MB - Last synced: 2 months ago - Pushed: about 2 years ago

powellgenomicslab/Nebulosa
R package to visualize gene expression data based on weighted kernel density estimation
  • * DESCRIPTION

Size: 264 KB - Last synced: 24 days ago - Pushed: 3 months ago

WarrenLab/single-cell
Pipelines and scripts for single-cell best practices
  • >= 3.1.4 DESCRIPTION

Size: 85.9 KB - Last synced: 8 months ago - Pushed: almost 2 years ago

CostaLab/CrossTalkeR
R package to do the Ligand Receptor Analysis Visualization
  • >= 4.0.3 DESCRIPTION

Size: 80.4 MB - Last synced: about 19 hours ago - Pushed: about 20 hours ago

carmonalab/scGate
marker-based purification of cell types from single-cell RNA-seq datasets
  • >= 4.0.0 DESCRIPTION

Size: 1.98 MB - Last synced: 4 days ago - Pushed: 5 days ago

scfurl/viewmaster
  • > 4.0.0 DESCRIPTION

Size: 7.29 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

bimberlabinternal/CellMembrane
An R package with wrappers and pipelines for single cell RNA-seq analysis
  • * DESCRIPTION

Size: 140 MB - Last synced: 1 day ago - Pushed: 1 day ago

immunogenomics/presto
Fast Wilcoxon and auROC
  • * DESCRIPTION

Size: 3.07 MB - Last synced: 2 months ago - Pushed: 2 months ago

huayc09/SeuratExtend
  • * DESCRIPTION

Size: 146 MB - Last synced: 15 days ago - Pushed: 15 days ago

yuabrahamliu/scDeconv
scDeconv is an R Package to Deconvolve Bulk DNA Methylation Data with scRNA-seq Data in a Multi-omics Manner.
  • >= 4.0.1 DESCRIPTION

Size: 116 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

MarcElosua/SPOTlight
Spatial Transcriptomics Capture Location Deconvolution
  • * DESCRIPTION

Size: 222 MB - Last synced: 13 days ago - Pushed: 2 months ago

stemangiola/tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
  • * DESCRIPTION

Size: 97.2 MB - Last synced: about 24 hours ago - Pushed: 2 days ago

decusInLabore/biologicSeqTools2
  • * DESCRIPTION

Size: 586 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

rpolicastro/scProportionTest
  • * DESCRIPTION

Size: 35.9 MB - Last synced: 9 months ago - Pushed: 9 months ago

decusInLabore/biologicViewerSC
  • * DESCRIPTION

Size: 15.3 MB - Last synced: 2 months ago - Pushed: 2 months ago

saezlab/dorothea
R package to access DoRothEA's regulons
  • * DESCRIPTION

Size: 393 MB - Last synced: 1 day ago - Pushed: 3 months ago

saezlab/progeny
R package for Pathway RespOnsive GENe activity inference
  • * DESCRIPTION

Size: 47.9 MB - Last synced: 2 days ago - Pushed: over 1 year ago

dynverse/dyngen
Simulating single-cell data using gene regulatory networks 📠
  • * DESCRIPTION

Size: 607 MB - Last synced: 20 days ago - Pushed: 3 months ago

carmonalab/UCell
An R package for single-cell gene signature scoring
  • * DESCRIPTION

Size: 30.8 MB - Last synced: about 1 month ago - Pushed: 2 months ago

WonLab-CS/Vesalius
Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data
  • * DESCRIPTION

Size: 147 MB - Last synced: 16 days ago - Pushed: 16 days ago

Byronxy/sc.utils
useful functions for single cell analysis
  • * DESCRIPTION

Size: 1.21 MB - Last synced: 2 months ago - Pushed: 2 months ago

DongqingSun96/MAESTRO Fork of liulab-dfci/MAESTRO
Single-cell Transcriptome and Regulome Analysis Pipeline
  • >= 4.0.0 DESCRIPTION

Size: 206 MB - Last synced: 7 months ago - Pushed: almost 3 years ago

msraredon/NICHES
Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  • * DESCRIPTION

Size: 91.3 MB - Last synced: 2 months ago - Pushed: 2 months ago

cancerbits/canceRbits
Wrapper and helper functions commonly used by the Developmental Cancer Genomics group at St. Anna Children's Cancer Research Institute
  • * DESCRIPTION

Size: 96.7 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

CostaLab/scMEGA
scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
  • * DESCRIPTION

Size: 127 MB - Last synced: 7 months ago - Pushed: 7 months ago

ZJUFanLab/SpaTalk
Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data
  • >= 3.0.0 DESCRIPTION

Size: 9.71 MB - Last synced: 3 months ago - Pushed: 11 months ago

NRCTM-bioinfo/HematoMap
  • * DESCRIPTION

Size: 64.2 MB - Last synced: 5 months ago - Pushed: 5 months ago

vitessce/vitessceR
R API and htmlwidget for Vitessce
  • * DESCRIPTION

Size: 49.2 MB - Last synced: 8 months ago - Pushed: 8 months ago

keita-iida/ASURAT
  • * DESCRIPTION

Size: 2.49 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

bimberlabinternal/RIRA
Code for utility of RIRA for classification of cell types/phenotypes
  • * DESCRIPTION

Size: 3.01 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

saeyslab/synthspot
synthspot: package to generate synthetic Visium-like spot data
  • * DESCRIPTION

Size: 6.8 MB - Last synced: 1 day ago - Pushed: 2 days ago

csangara/synthvisium
synthvisium: package to generate synthetic Visium-like spot data
  • * DESCRIPTION

Size: 6.78 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

arc85/celltalker
Inference of cell-cell communication from single-cell RNAseq data
  • >= 2.3.0 DESCRIPTION

Size: 11.1 MB - Last synced: 3 months ago - Pushed: 11 months ago

satijalab/azimuth
A Shiny web app for mapping datasets using Seurat v4
  • >= 4.0.0 DESCRIPTION

Size: 7.51 MB - Last synced: 6 days ago - Pushed: about 1 month ago

CostaLab/MOJITOO
MOJITOO: a fast and universal method for integration of multimodal single cell data
  • >= 3.2.3 DESCRIPTION

Size: 3.39 MB - Last synced: 8 months ago - Pushed: 8 months ago

aerickso/SpatialInferCNV
Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  • * DESCRIPTION

Size: 135 MB - Last synced: 24 days ago - Pushed: over 1 year ago

edward130603/BayesSpace
Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.
  • * DESCRIPTION

Size: 548 MB - Last synced: 29 days ago - Pushed: about 1 month ago

mojaveazure/seurat-disk
Interfaces for HDF5-based Single Cell File Formats
  • >= 3.2.0 DESCRIPTION

Size: 551 KB - Last synced: 4 months ago - Pushed: 7 months ago

romanhaa/Cerebro
Visualization of scRNA-seq data.
  • >= 2.3.0 source/Windows/R-Portable-Win/library/cerebroApp/DESCRIPTION

Size: 2.99 GB - Last synced: 3 months ago - Pushed: over 1 year ago

sistia01/DWLS
Dampened Weighted Least Squares
  • * DESCRIPTION

Size: 391 MB - Last synced: 6 months ago - Pushed: almost 2 years ago

InfOmics/stardust
  • * DESCRIPTION

Size: 1.31 GB - Last synced: about 1 year ago - Pushed: about 2 years ago

andreaskapou/SeuratPipe
Packaging common Seurat analysis tasks for reproducible research
  • * DESCRIPTION

Size: 6.46 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

vertesy/ggExpress
ggExpress is the fastest way to create, annotate and and save plots in R.
  • * DESCRIPTION

Size: 424 KB - Last synced: about 1 month ago - Pushed: about 1 month ago

zhanglhbioinfor/DIRECT-NET
  • >= 4.0 DESCRIPTION

Size: 2.17 MB - Last synced: 11 months ago - Pushed: 12 months ago

CompEpigen/scMethrix
An R 📦 for fast and flexible scDNA methylation analysis
  • * DESCRIPTION

Size: 30.9 MB - Last synced: 9 months ago - Pushed: about 2 years ago

jbergenstrahle/STUtility
  • >= 3.0.0 DESCRIPTION

Size: 130 MB - Last synced: 2 months ago - Pushed: about 1 year ago

ComunidadBioInfo/cdsb2021_scRNAseq
Taller de la CDSB 2021 sobre análisis de datos de scRNA-seq con Bioconductor
  • * DESCRIPTION

Size: 111 MB - Last synced: 2 months ago - Pushed: 8 months ago

shangll123/SpatialPCA
Spatially aware dimension reduction for spatial transcriptomics.
  • * DESCRIPTION

Size: 16 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

mgildea87/CVRCFunc
  • * DESCRIPTION

Size: 3.6 MB - Last synced: 5 months ago - Pushed: 5 months ago

romanhaa/cerebroApp
R package containing the Cerebro application.
  • >= 3.0.0 DESCRIPTION

Size: 22.4 MB - Last synced: 7 months ago - Pushed: over 2 years ago