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Topic: Transcription or Clustering or Metabolomics

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Release: Release 3.4 (2016)

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237 packages on Bioconductor tagged Transcription or Clustering or Metabolomics, most distinct IPs first

Transcription, Clustering and Metabolomics 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
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
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
graphite
GRAPH Interaction from pathway Topological EnvironmentGabriele Sales		Gabriele Salessoftware28 Apr 20267,01248
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
mzR
parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)Steffen Neumann		Steffen Neumannsoftware28 Apr 20265,63915
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
monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqCole Trapnell		Cole Trapnellsoftware28 Apr 20264,48574
ConsensusClusterPlus
ConsensusClusterPlusMatt Wilkerson		Matt Wilkersonsoftware28 Apr 20263,96510
xcms
LC-MS and GC-MS Data AnalysisSteffen Neumann		Steffen Neumannsoftware7 Jul 20263,537143
ropls
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics dataEtienne A. Thevenot		Etienne A. Thevenotsoftware28 Apr 20262,96997
metagenomeSeq
Statistical analysis for sparse high-throughput sequencingJoseph N. Paulson		Joseph N. Paulsonsoftware28 Apr 20262,92432
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
ChemmineR
Cheminformatics Toolkit for RThomas Girke		Thomas Girkesoftware28 Apr 20261,85465
pRoloc
A unifying bioinformatics framework for spatial proteomicsLisa Breckels		Lisa Breckelssoftware28 Apr 20261,689230
MLInterfaces
Uniform interfaces to R machine learning procedures for data in Bioconductor containersVincent Carey		Vincent Careysoftware28 Apr 20261,628120
genefu
Computation of Gene Expression-Based Signatures in Breast CancerBenjamin Haibe-Kains		Benjamin Haibe-Kainssoftware28 Apr 20261,619116
CAMERA
Collection of annotation related methods for mass spectrometry dataSteffen Neumann		Steffen Neumannsoftware28 Apr 20261,548157