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Topic: Transcription or Proteomics

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Release: Release 3.6 (2017)

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207 packages on Bioconductor tagged Transcription or Proteomics, most distinct IPs first

Transcription and Proteomics 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
DESeq2
Differential gene expression analysis based on the negative binomial distributionMichael Love		Michael Lovesoftware28 Apr 202632,07254
ProtGenerics
Generic infrastructure for Bioconductor mass spectrometry packagesLaurent Gatto		Laurent Gattosoftware28 Apr 202613,0181
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
MSnbase
Base Functions and Classes for Mass Spectrometry and ProteomicsLaurent Gatto		Laurent Gattosoftware9 Aug 20265,521134
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
mzID
An mzIdentML parser for RLaurent Gatto		Laurent Gattosoftware28 Apr 20264,53211
MassSpecWavelet
Peak Detection for Mass Spectrometry data using wavelet-based algorithmsSergio Oller Moreno		Sergio Oller Morenosoftware7 Jul 20263,0960
ropls
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics dataEtienne A. Thevenot		Etienne A. Thevenotsoftware28 Apr 20262,96997
goseq
Gene Ontology analyser for RNA-seq and other length biased dataFederico Marini		Federico Marinisoftware28 Apr 20262,404104
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
MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics ExperimentsMeena Choi		Meena Choisoftware28 Apr 20261,586100
qpgraph
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics DataRobert Castelo		Robert Castelosoftware28 Apr 20261,49581
IsoformSwitchAnalyzeR
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq dataKristoffer Vitting-Seerup		Kristoffer Vitting-Seerupsoftware28 Apr 20261,421151
Cardinal
A mass spectrometry imaging toolbox for statistical analysisKylie Ariel Bemis		Kylie Ariel Bemissoftware28 Apr 20261,40531
hpar
Human Protein Atlas in RLaurent Gatto		Laurent Gattosoftware28 Apr 20261,38264
SC3
Single-Cell Consensus ClusteringVladimir Kiselev		Vladimir Kiselevsoftware28 Apr 20261,36892
rpx
R Interface to the ProteomeXchange RepositoryLaurent Gatto		Laurent Gattosoftware29 Sep 20261,32946
scmap
A tool for unsupervised projection of single cell RNA-seq dataVladimir Kiselev		Vladimir Kiselevsoftware28 Apr 20261,27062
MSnID
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics IdentificationsVlad Petyuk		Vlad Petyuksoftware28 Apr 20261,236169
SGSeq
Splice event prediction and quantification from RNA-seq dataLeonard Goldstein		Leonard Goldsteinsoftware28 Apr 20261,22780
TPP
Analyze thermal proteome profiling (TPP) experimentsDorothee Childs		Dorothee Childssoftware14 Sep 20261,22186
affylmGUI
GUI for limma Package with Affymetrix MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 20261,19455
qcmetrics
A Framework for Quality ControlLaurent Gatto		Laurent Gattosoftware28 Apr 20261,19020
scde
Single Cell Differential ExpressionEvan Biederstedt		Evan Biederstedtsoftware28 Apr 20261,17950