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Topic: Transcription or AffymetrixChip or Clustering

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Release: Release 3.8 (2018)

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637 packages on Bioconductor tagged Transcription or AffymetrixChip or Clustering, most distinct IPs first

Transcription, AffymetrixChip and Clustering 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
BiocNeighbors
Nearest Neighbor Detection for Bioconductor PackagesAaron Lun		Aaron Lunsoftware28 Apr 202616,61924
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
EnhancedVolcano
Publication-ready volcano plots with enhanced colouring and labelingJared Andrews		Jared Andrewssoftware28 Apr 20267,62025
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
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
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
monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqCole Trapnell		Cole Trapnellsoftware28 Apr 20264,48574
hgu133plus2.db
Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record4,22743
ConsensusClusterPlus
ConsensusClusterPlusMatt Wilkerson		Matt Wilkersonsoftware28 Apr 20263,96510
metagenomeSeq
Statistical analysis for sparse high-throughput sequencingJoseph N. Paulson		Joseph N. Paulsonsoftware28 Apr 20262,92432
tximeta
Transcript Quantification Import with Automatic MetadataMichael Love		Michael Lovesoftware26 Oct 20262,485108
goseq
Gene Ontology analyser for RNA-seq and other length biased dataFederico Marini		Federico Marinisoftware28 Apr 20262,404104
Mfuzz
Soft clustering of omics time series dataMatthias Futschik		Matthias Futschiksoftware28 Apr 20262,35316
flowClust
Clustering for Flow CytometryGreg Finak		Greg Finaksoftware28 Apr 20262,26624
FlowSOM
Using self-organizing maps for visualization and interpretation of cytometry dataSofie Van Gassen		Sofie Van Gassensoftware28 Apr 20262,139112
destiny
Creates diffusion mapsPhilipp Angerer		Philipp Angerersoftware28 Apr 20262,01584
hgu133a.db
Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record1,99643
ChemmineR
Cheminformatics Toolkit for RThomas Girke		Thomas Girkesoftware28 Apr 20261,85465
RcisTarget
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regionsGert Hulselmans		Gert Hulselmanssoftwareno date on record1,724