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Topic: Spatial or StatisticalMethod or Transcription

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Release: Release 3.6 (2017)

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565 packages on Bioconductor tagged Spatial or StatisticalMethod or Transcription, most distinct IPs first

Spatial, StatisticalMethod and Transcription in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
limma
Linear Models for Microarray and Omics DataGordon Smyth		Gordon Smythsoftware10 Aug 202645,9656
ggtree
an R package for visualization of tree and annotation dataGuangchuang Yu		Guangchuang Yusoftware29 Oct 202634,37279
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202632,39210
DESeq2
Differential gene expression analysis based on the negative binomial distributionMichael Love		Michael Lovesoftware28 Apr 202632,07254
treeio
Base Classes and Functions for Phylogenetic Tree Input and OutputGuangchuang Yu		Guangchuang Yusoftware30 Apr 202631,96639
clusterProfiler
A Universal Enrichment Tool for Interpreting Omics DataGuangchuang Yu		Guangchuang Yusoftware19 Oct 202629,661138
GOSemSim
GO-terms Semantic Similarity MeasuresGuangchuang Yu		Guangchuang Yusoftware30 Jun 202627,49548
graph
graph: A package to handle graph data structuresBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202625,6557
GSEABase
Gene set enrichment data structures and methodsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202613,34446
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202612,63578
Rgraphviz
Provides plotting capabilities for R graph objectsKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 202611,26310
sva
Surrogate Variable AnalysisJeffrey T. Leek		Jeffrey T. Leeksoftware5 May 202610,80468
RBGL
An interface to the BOOST graph libraryBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202610,6989
scran
Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202610,13962
phyloseq
Handling and analysis of high-throughput microbiome census dataPaul J. McMurdie		Paul J. McMurdiesoftware28 Apr 20268,37966
apeglm
Approximate posterior estimation for GLM coefficientsAnqi Zhu		Anqi Zhusoftware28 Apr 20267,71636
pcaMethods
A collection of PCA methodsHenning Redestig		Henning Redestigsoftware28 Apr 20267,38510
graphite
GRAPH Interaction from pathway Topological EnvironmentGabriele Sales		Gabriele Salessoftware28 Apr 20267,01248
KEGGgraph
KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorJitao David Zhang		Jitao David Zhangsoftware28 Apr 20266,80714
TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC dataTiago Chedraoui Silva		Tiago Chedraoui Silvasoftware28 Apr 20266,750103
DirichletMultinomial
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome DataMartin Morgan		Martin Morgansoftware28 Sep 20266,4909
tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysisMichael Love		Michael Lovesoftware28 Apr 20265,8043
pathview
a tool set for pathway based data integration and visualizationWeijun Luo		Weijun Luosoftware28 Apr 20265,70650
DECIPHER
Tools for curating, analyzing, and manipulating biological sequencesErik Wright		Erik Wrightsoftware30 Jul 20264,88216
TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) AnalysisGe Tan		Ge Tansoftware28 Apr 20264,72179
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
monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqCole Trapnell		Cole Trapnellsoftware28 Apr 20264,48574
dada2
Accurate, high-resolution sample inference from amplicon sequencing dataBenjamin Callahan		Benjamin Callahansoftware28 Apr 20264,20675
ConsensusClusterPlus
ConsensusClusterPlusMatt Wilkerson		Matt Wilkersonsoftware28 Apr 20263,96510
maftools
Summarize, Analyze and Visualize MAF FilesAnand Mayakonda		Anand Mayakondasoftware28 Apr 20263,52326