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Topic: SingleCell or Proteomics

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Release: Release 3.6 (2017)

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138 packages on Bioconductor tagged SingleCell or Proteomics, most distinct IPs first

SingleCell 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
SingleCellExperiment
S4 Classes for Single Cell DataDavide Risso		Davide Rissosoftware28 Apr 202624,48325
HDF5Array
HDF5 datasets as array-like objects in RHervé Pagès		Hervé Pagèssoftware28 Apr 202620,53728
ProtGenerics
Generic infrastructure for Bioconductor mass spectrometry packagesLaurent Gatto		Laurent Gattosoftware28 Apr 202613,0181
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202612,63578
scran
Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202610,13962
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
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
MAST
Model-based Analysis of Single Cell TranscriptomicsAndrew McDavid		Andrew McDavidsoftware28 Apr 20263,74056
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
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
chromVAR
Chromatin Variation Across RegionsAlicia Schep		Alicia Schepsoftware11 May 20262,255134
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
zinbwave
Zero-Inflated Negative Binomial Model for RNA-Seq DataDavide Risso		Davide Rissosoftware28 Apr 20261,56974
splatter
Simple Simulation of Single-cell RNA Sequencing DataLuke Zappia		Luke Zappiasoftware28 Apr 20261,55361
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
CATALYST
Cytometry dATa anALYSis ToolsHelena L. Crowell		Helena L. Crowellsoftware28 Apr 20261,265176
MSnID
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics IdentificationsVlad Petyuk		Vlad Petyuksoftware28 Apr 20261,236169
TPP
Analyze thermal proteome profiling (TPP) experimentsDorothee Childs		Dorothee Childssoftware14 Sep 20261,22186