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Topic: Spatial or Transcriptomics

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Release: Release 3.21 (2025)

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296 packages on Bioconductor tagged Spatial or Transcriptomics, most distinct IPs first

Spatial and Transcriptomics in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
limma
Linear Models for Microarray and Omics DataGordon Smyth		Gordon Smythsoftware10 Aug 202645,9656
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202632,39210
scuttle
Legacy Utilities for Single-Cell RNA-Seq AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202614,23639
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202612,63578
bluster
Clustering Algorithms for BioconductorAaron Lun		Aaron Lunsoftware28 Apr 202610,90344
SpatialExperiment
S4 Class for Spatially Resolved -omics DataDario Righelli		Dario Righellisoftware28 Apr 202610,71864
scran
Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202610,13962
SingleR
Reference-Based Single-Cell RNA-Seq AnnotationAaron Lun		Aaron Lunsoftware10 Sep 20266,76128
tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysisMichael Love		Michael Lovesoftware28 Apr 20265,8043
batchelor
Single-Cell Batch Correction MethodsAaron Lun		Aaron Lunsoftware28 Apr 20265,72056
slingshot
Tools for ordering single-cell sequencingKelly Street		Kelly Streetsoftware28 Apr 20264,68438
AUCell
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)Gert Hulselmans		Gert Hulselmanssoftware29 Apr 20264,610115
DropletUtils
Utilities for Handling Single-Cell Droplet DataJonathan Griffiths		Jonathan Griffithssoftware27 Sep 20264,10759
UCell
Rank-based signature enrichment analysis for single-cell dataMassimo Andreatta		Massimo Andreattasoftware28 Apr 20263,92441
MAST
Model-based Analysis of Single Cell TranscriptomicsAndrew McDavid		Andrew McDavidsoftware28 Apr 20263,74056
topGO
Enrichment Analysis for Gene OntologyFederico Marini		Federico Marinisoftware28 Apr 20263,22848
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20263,21199
scrapper
Bindings to C++ Libraries for Single-Cell AnalysisAaron Lun		Aaron Lunsoftware19 May 20263,11930
ropls
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics dataEtienne A. Thevenot		Etienne A. Thevenotsoftware28 Apr 20262,96997
infercnv
Infer Copy Number Variation from Single-Cell RNA-Seq DataChristophe Georgescu		Christophe Georgescusoftware28 Apr 20262,709194
OmnipathR
OmniPath web service client and moreDenes Turei		Denes Tureisoftware30 Apr 20262,68589
ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor		Greg Gloorsoftware28 Apr 20262,53356
tximeta
Transcript Quantification Import with Automatic MetadataMichael Love		Michael Lovesoftware26 Oct 20262,485108
tradeSeq
trajectory-based differential expression analysis for sequencing dataHector Roux de Bezieux		Hector Roux de Bezieuxsoftware28 Apr 20262,46073
dittoSeq
User Friendly Single-Cell and Bulk RNA Sequencing VisualizationDaniel Bunis		Daniel Bunissoftware28 Apr 20261,83155
quantiseqr
Quantification of the Tumor Immune contexture from RNA-seq dataFederico Marini		Federico Marinisoftware28 Apr 20261,72758
RcisTarget
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regionsGert Hulselmans		Gert Hulselmanssoftwareno date on record1,724
zinbwave
Zero-Inflated Negative Binomial Model for RNA-Seq DataDavide Risso		Davide Rissosoftware28 Apr 20261,56974
splatter
Simple Simulation of Single-cell RNA Sequencing DataLuke Zappia		Luke Zappiasoftware28 Apr 20261,55361
scds
In-Silico Annotation of Doublets for Single Cell RNA Sequencing DataDennis Kostka		Dennis Kostkasoftware28 Apr 20261,49745