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Topic: Transcription or Metabolomics or Clustering

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Release: Release 3.16 (2022)

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

Transcription, Metabolomics 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
bluster
Clustering Algorithms for BioconductorAaron Lun		Aaron Lunsoftware28 Apr 202610,90344
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
graphite
GRAPH Interaction from pathway Topological EnvironmentGabriele Sales		Gabriele Salessoftware28 Apr 20267,01248
SingleR
Reference-Based Single-Cell RNA-Seq AnnotationAaron Lun		Aaron Lunsoftware10 Sep 20266,76128
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
mixOmics
Omics Data Integration ProjectDerek Lei		Derek Leisoftware28 Apr 20265,37083
MsCoreUtils
Core Utils for Mass Spectrometry DataRforMassSpectrometry Package Maintainer		RforMassSpectrometry Package Maintainersoftware28 Apr 20265,02413
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
QFeatures
Quantitative features for mass spectrometry dataLaurent Gatto		Laurent Gattosoftware28 Apr 20264,54099
monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqCole Trapnell		Cole Trapnellsoftware28 Apr 20264,48574
Spectra
Spectra Infrastructure for Mass Spectrometry DataRforMassSpectrometry Package Maintainer		RforMassSpectrometry Package Maintainersoftware9 Jun 20264,46530
ConsensusClusterPlus
ConsensusClusterPlusMatt Wilkerson		Matt Wilkersonsoftware28 Apr 20263,96510
MetaboCoreUtils
Core Utils for Metabolomics DataJohannes Rainer		Johannes Rainersoftware30 Apr 20263,94024
decoupleR
decoupleR: Ensemble of computational methods to infer biological activities from omics dataPau Badia-i-Mompel		Pau Badia-i-Mompelsoftware30 Oct 20253,63441