bioconductor.org "Proteomics" keyword
View the packages on the bioconductor.org package registry that are tagged with the "Proteomics" keyword.
artMS 1.26.0
Analytical R tools for Mass Spectrometry5 versions - Latest release: 3 months ago - 13.6 thousand downloads total - 1 maintainer
Pviz 1.42.0
Peptide Annotation and Data Visualization using Gviz5 versions - Latest release: 3 months ago - 1 dependent package - 21.1 thousand downloads total - 1 maintainer
MSstatsQCgui 1.28.0
A graphical user interface for MSstatsQC package5 versions - Latest release: 3 months ago - 10.6 thousand downloads total - 1 maintainer
MSstatsConvert 1.18.0
Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format7 versions - Latest release: 3 months ago - 6 dependent packages - 28.7 thousand downloads total - 1 maintainer
DIAlignR 2.16.0
Dynamic Programming Based Alignment of MS2 Chromatograms5 versions - Latest release: 3 months ago - 6.81 thousand downloads total - 6 stars on GitHub - 1 maintainer
deltaGseg 1.48.0
deltaGseg5 versions - Latest release: 3 months ago - 23.2 thousand downloads total - 1 maintainer
phosphonormalizer 1.32.0
Compensates for the bias introduced by median normalization in5 versions - Latest release: 3 months ago - 12.7 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
5 versions - Latest release: 3 months ago - 2 dependent packages - 41.2 thousand downloads total - 13 stars on GitHub - 1 maintainer
cleaver 1.46.0
Cleavage of Polypeptide Sequences5 versions - Latest release: 3 months ago - 2 dependent packages - 41.2 thousand downloads total - 13 stars on GitHub - 1 maintainer
PhosR 1.18.1
A set of methods and tools for comprehensive analysis of phosphoproteomics data6 versions - Latest release: about 2 months ago - 10.4 thousand downloads total - 1 maintainer
HPiP 1.14.0
Host-Pathogen Interaction Prediction5 versions - Latest release: 3 months ago - 6.05 thousand downloads total - 3 stars on GitHub - 1 maintainer
ProteoDisco 1.14.0
Generation of customized protein variant databases from genomic variants, splice-junctions and ma...5 versions - Latest release: 3 months ago - 5.89 thousand downloads total - 5 stars on GitHub - 1 maintainer
SubCellBarCode 1.24.0
SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome5 versions - Latest release: 3 months ago - 9.23 thousand downloads total - 1 maintainer
KinSwingR 1.26.0
KinSwingR: network-based kinase activity prediction5 versions - Latest release: 3 months ago - 9.46 thousand downloads total - 1 maintainer
CNORfeeder 1.48.0
Integration of CellNOptR to add missing links5 versions - Latest release: 3 months ago - 26.1 thousand downloads total - 1 maintainer
scp 1.18.0
Mass Spectrometry-Based Single-Cell Proteomics Data Analysis5 versions - Latest release: 3 months ago - 11.5 thousand downloads total - 26 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 20 dependent packages - 1.22 million downloads total - 7 stars on GitHub - 1 maintainer
ProtGenerics 1.40.0
Generic infrastructure for Bioconductor mass spectrometry packages5 versions - Latest release: 3 months ago - 20 dependent packages - 1.22 million downloads total - 7 stars on GitHub - 1 maintainer
MSstatsLOBD 1.16.0
Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)5 versions - Latest release: 3 months ago - 5.97 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 6.3% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 59.8 thousand downloads total - 1 maintainer
DEP 1.30.0
Differential Enrichment analysis of Proteomics data5 versions - Latest release: 3 months ago - 1 dependent package - 59.8 thousand downloads total - 1 maintainer
SWATH2stats 1.38.0
Transform and Filter SWATH Data for Statistical Packages6 versions - Latest release: 3 months ago - 18.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
6 versions - Latest release: 3 months ago - 1 dependent package - 34.5 thousand downloads total - 1 maintainer
EGSEA 1.36.0
Ensemble of Gene Set Enrichment Analyses6 versions - Latest release: 3 months ago - 1 dependent package - 34.5 thousand downloads total - 1 maintainer
SMAD 1.24.0
Statistical Modelling of AP-MS Data (SMAD)5 versions - Latest release: 3 months ago - 8.79 thousand downloads total - 1 maintainer
clippda 1.58.0
A package for the clinical proteomic profiling data analysis5 versions - Latest release: 3 months ago - 32.4 thousand downloads total - 1 maintainer
Top 7.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 2 dependent packages - 42.6 thousand downloads total - 1 maintainer
msmsEDA 1.46.0
Exploratory Data Analysis of LC-MS/MS data by spectral counts5 versions - Latest release: 3 months ago - 2 dependent packages - 42.6 thousand downloads total - 1 maintainer
timeOmics 1.20.0
Time-Course Multi-Omics data integration5 versions - Latest release: 3 months ago - 1 dependent package - 9.42 thousand downloads total - 21 stars on GitHub - 1 maintainer
SDAMS 1.28.0
Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequen...5 versions - Latest release: 3 months ago - 11.7 thousand downloads total - 1 maintainer
drawProteins 1.28.0
Package to Draw Protein Schematics from Uniprot API output6 versions - Latest release: 3 months ago - 1 dependent package - 20.8 thousand downloads total - 34 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
5 versions - Latest release: 3 months ago - 9 dependent packages - 594 thousand downloads total - 41 stars on GitHub - 1 maintainer
pathview 1.48.0
a tool set for pathway based data integration and visualization5 versions - Latest release: 3 months ago - 9 dependent packages - 594 thousand downloads total - 41 stars on GitHub - 1 maintainer
PRONE 1.2.1
The PROteomics Normalization Evaluator5 versions - Latest release: 29 days ago - 2.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
mitch 1.20.0
Multi-Contrast Gene Set Enrichment Analysis7 versions - Latest release: 3 months ago - 8.59 thousand downloads total - 16 stars on GitHub - 1 maintainer
statTarget 1.38.0
Statistical Analysis of Molecular Profiles5 versions - Latest release: 3 months ago - 26.7 thousand downloads total - 1 maintainer
MSstatsTMT 2.16.0
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tande...7 versions - Latest release: 3 months ago - 2 dependent packages - 24.3 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 59.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
fmcsR 1.50.0
Mismatch Tolerant Maximum Common Substructure Searching5 versions - Latest release: 3 months ago - 1 dependent package - 59.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
5 versions - Latest release: 3 months ago - 5 dependent packages - 324 thousand downloads total - 1 maintainer
mzID 1.46.0
An mzIdentML parser for R5 versions - Latest release: 3 months ago - 5 dependent packages - 324 thousand downloads total - 1 maintainer
wpm 1.18.0
Well Plate Maker5 versions - Latest release: 3 months ago - 7.78 thousand downloads total - 5 stars on GitHub - 1 maintainer
CNORdt 1.50.0
Add-on to CellNOptR: Discretized time treatments5 versions - Latest release: 3 months ago - 25.8 thousand downloads total - 1 maintainer
Doscheda 1.30.0
A DownStream Chemo-Proteomics Analysis Pipeline5 versions - Latest release: 3 months ago - 12.8 thousand downloads total - 1 maintainer
Pirat 1.2.0
Precursor or Peptide Imputation under Random Truncation4 versions - Latest release: 3 months ago - 2.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
customProDB 1.48.0
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics ...6 versions - Latest release: 3 months ago - 30.7 thousand downloads total - 1 maintainer
limpa 1.0.5
Quantification and Differential Analysis of Proteomics Data3 versions - Latest release: 29 days ago - 999 downloads total - 1 maintainer
AssessORF 1.26.0
Assess Gene Predictions Using Proteomics and Evolutionary Conservation5 versions - Latest release: 3 months ago - 13.2 thousand downloads total - 1 maintainer
QuartPAC 1.40.0
Identification of mutational clusters in protein quaternary structures5 versions - Latest release: 3 months ago - 15.1 thousand downloads total - 1 maintainer
Top 8.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 32.9 thousand downloads total - 1 maintainer
PLPE 1.68.0
Local Pooled Error Test for Differential Expression with Paired High-throughput Data5 versions - Latest release: 3 months ago - 32.9 thousand downloads total - 1 maintainer
Top 5.0% on bioconductor.org
7 versions - Latest release: 3 months ago - 19 dependent packages - 227 thousand downloads total - 17 stars on GitHub - 1 maintainer
MsCoreUtils 1.20.0
Core Utils for Mass Spectrometry Data7 versions - Latest release: 3 months ago - 19 dependent packages - 227 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 4.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 64.6 thousand downloads total - 1 maintainer
PROcess 1.84.0
Ciphergen SELDI-TOF Processing5 versions - Latest release: 3 months ago - 64.6 thousand downloads total - 1 maintainer
MSstatsLiP 1.14.1
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments8 versions - Latest release: 29 days ago - 6.46 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 6.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 3 dependent packages - 60.8 thousand downloads total - 1 maintainer
hpar 1.50.0
Human Protein Atlas in R5 versions - Latest release: 3 months ago - 3 dependent packages - 60.8 thousand downloads total - 1 maintainer
proBAMr 1.42.0
Generating SAM file for PSMs in shotgun proteomics data5 versions - Latest release: 3 months ago - 19.3 thousand downloads total - 1 maintainer
DEqMS 1.26.0
a tool to perform statistical analysis of differential protein expression for quantitative proteo...5 versions - Latest release: 3 months ago - 20.2 thousand downloads total - 17 stars on GitHub - 1 maintainer
omicRexposome 1.30.0
Exposome and omic data associatin and integration analysis6 versions - Latest release: 3 months ago - 12.6 thousand downloads total - 1 maintainer
NPARC 1.20.0
Non-parametric analysis of response curves for thermal proteome profiling experiments5 versions - Latest release: 3 months ago - 9.08 thousand downloads total - 1 maintainer
SBGNview 1.22.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"5 versions - Latest release: 3 months ago - 13.6 thousand downloads total - 26 stars on GitHub - 1 maintainer
QFeatures 1.18.0
Quantitative features for mass spectrometry data7 versions - Latest release: 3 months ago - 6 dependent packages - 89.8 thousand downloads total - 27 stars on GitHub - 1 maintainer
CONSTANd 1.16.0
Data normalization by matrix raking5 versions - Latest release: 3 months ago - 6.85 thousand downloads total - 1 maintainer
MSstatsQC 2.26.0
Longitudinal system suitability monitoring and quality control for proteomic experiments5 versions - Latest release: 3 months ago - 1 dependent package - 13.8 thousand downloads total - 1 maintainer
biosigner 1.36.0
Signature discovery from omics data5 versions - Latest release: 3 months ago - 2 dependent packages - 20.2 thousand downloads total - 1 maintainer
Top 3.1% on bioconductor.org
5 versions - Latest release: 3 months ago - 4 dependent packages - 114 thousand downloads total - 1 maintainer
RankProd 3.34.0
Rank Product method for identifying differentially expressed genes with application in meta-analysis5 versions - Latest release: 3 months ago - 4 dependent packages - 114 thousand downloads total - 1 maintainer
CausalR 1.40.0
Causal network analysis methods5 versions - Latest release: 3 months ago - 17.4 thousand downloads total - 2 maintainers
Top 8.9% on bioconductor.org
5 versions - Latest release: 3 months ago - 6 dependent packages - 43.2 thousand downloads total - 1 maintainer
CellNOptR 1.54.0
Training of boolean logic models of signalling networks using prior knowledge networks and pertur...5 versions - Latest release: 3 months ago - 6 dependent packages - 43.2 thousand downloads total - 1 maintainer
NanoStringNCTools 1.15.0
NanoString nCounter Tools6 versions - Latest release: 3 months ago - 2 dependent packages - 22.7 thousand downloads total - 1 maintainer
idpr 1.18.0
Profiling and Analyzing Intrinsically Disordered Proteins in R5 versions - Latest release: 2 months ago - 8.06 thousand downloads total - 4 stars on GitHub - 1 maintainer
PSMatch 1.12.0
Handling and Managing Peptide Spectrum Matches5 versions - Latest release: 3 months ago - 2 dependent packages - 48.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
msImpute 1.18.0
Imputation of label-free mass spectrometry peptides5 versions - Latest release: 3 months ago - 10.9 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 7.9% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 42.2 thousand downloads total - 1 maintainer
msmsTests 1.46.0
LC-MS/MS Differential Expression Tests5 versions - Latest release: 3 months ago - 1 dependent package - 42.2 thousand downloads total - 1 maintainer
Prostar 1.40.0
Provides a GUI for DAPAR11 versions - Latest release: 3 months ago - 22.9 thousand downloads total - 1 maintainer
cytoMEM 1.12.0
Marker Enrichment Modeling (MEM)5 versions - Latest release: 3 months ago - 6.43 thousand downloads total - 0 stars on GitHub - 1 maintainer
rain 1.42.0
Rhythmicity Analysis Incorporating Non-parametric Methods5 versions - Latest release: 3 months ago - 24.1 thousand downloads total - 1 maintainer
cisPath 1.47.0
Visualization and management of the protein-protein interaction networks.5 versions - Latest release: 3 months ago - 24.9 thousand downloads total - 1 maintainer
cydar 1.32.1
Using Mass Cytometry for Differential Abundance Analyses6 versions - Latest release: about 2 months ago - 17.6 thousand downloads total - 1 maintainer
PAA 1.42.0
PAA (Protein Array Analyzer)5 versions - Latest release: 3 months ago - 22.3 thousand downloads total - 2 maintainers
Top 8.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 41.9 thousand downloads total - 1 maintainer
MSnID 1.42.0
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications5 versions - Latest release: 3 months ago - 41.9 thousand downloads total - 1 maintainer
roastgsa 1.6.0
Rotation based gene set analysis4 versions - Latest release: 3 months ago - 3.81 thousand downloads total - 0 stars on GitHub - 1 maintainer
EWCE 1.16.0
Expression Weighted Celltype Enrichment6 versions - Latest release: 2 months ago - 15.6 thousand downloads total - 53 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
7 versions - Latest release: 3 months ago - 3 dependent packages - 63.3 thousand downloads total - 16 stars on GitHub - 1 maintainer
pRoloc 1.48.0
A unifying bioinformatics framework for spatial proteomics7 versions - Latest release: 3 months ago - 3 dependent packages - 63.3 thousand downloads total - 16 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
5 versions - Latest release: 3 months ago - 9 dependent packages - 109 thousand downloads total - 1 maintainer
ropls 1.40.0
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data5 versions - Latest release: 3 months ago - 9 dependent packages - 109 thousand downloads total - 1 maintainer
RolDE 1.12.0
RolDE: Robust longitudinal Differential Expression5 versions - Latest release: 3 months ago - 5.59 thousand downloads total - 5 stars on GitHub - 1 maintainer
PolySTest 1.2.0
PolySTest: Detection of differentially regulated features. Combined statistical testing for data ...3 versions - Latest release: 3 months ago - 1.71 thousand downloads total - 0 stars on GitHub - 1 maintainer
pathwayPCA 1.24.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection5 versions - Latest release: 3 months ago - 1 dependent package - 11.6 thousand downloads total - 11 stars on GitHub - 1 maintainer
fenr 1.6.1
Fast functional enrichment for interactive applications11 versions - Latest release: about 1 month ago - 4.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
6 versions - Latest release: 3 months ago - 3 dependent packages - 59.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
rpx 2.16.0
R Interface to the ProteomeXchange Repository6 versions - Latest release: 3 months ago - 3 dependent packages - 59.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
synapter 2.31.0
Label-free data analysis pipeline for optimal identification and quantitation5 versions - Latest release: 3 months ago - 34.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
HPAanalyze 1.26.1
Retrieve and analyze data from the Human Protein Atlas6 versions - Latest release: about 2 months ago - 14.3 thousand downloads total - 36 stars on GitHub - 1 maintainer
MQmetrics 1.14.0 removed
Quality Control of Protemics Data4 versions - Latest release: 8 months ago - 2.92 thousand downloads total - 1 maintainer
proBatch 1.15.1 removed
Tools for Diagnostics and Corrections of Batch Effects in Proteomics1 version - Latest release: almost 2 years ago - 5.93 thousand downloads total - 14 stars on GitHub - 1 maintainer
MobilityTransformR 1.8.0 removed
Effective mobility scale transformation of CE-MS(/MS) data3 versions - Latest release: about 1 year ago - 2.31 thousand downloads total - 2 stars on GitHub - 1 maintainer
InterMineR 1.26.0 removed
R Interface with InterMine-Powered Databases4 versions - Latest release: about 1 year ago - 12 thousand downloads total - 17 stars on GitHub - 1 maintainer
phemd 1.20.0 removed
Phenotypic EMD for comparison of single-cell samples3 versions - Latest release: about 1 year ago - 5.76 thousand downloads total - 1 maintainer
OmicsLonDA 1.18.0 removed
Omics Longitudinal Differential Analysis2 versions - Latest release: over 1 year ago - 5.95 thousand downloads total - 5 stars on GitHub - 1 maintainer
deco 1.18.0 removed
Decomposing Heterogeneous Cohorts using Omic Data Profiling2 versions - Latest release: over 1 year ago - 4.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 9.6% on bioconductor.org
2 versions - Latest release: over 1 year ago - 26.7 thousand downloads total - 1 maintainer
LPEadj 1.62.0 removed
A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment...2 versions - Latest release: over 1 year ago - 26.7 thousand downloads total - 1 maintainer
MSstatsSampleSize 1.16.0 removed
Simulation tool for optimal design of high-dimensional MS-based proteomics experiment2 versions - Latest release: over 1 year ago - 3.89 thousand downloads total - 1 maintainer
proFIA 1.26.0 removed
Preprocessing of FIA-HRMS data1 version - Latest release: almost 2 years ago - 8.96 thousand downloads total - 1 maintainer
pulsedSilac 1.14.0 removed
Analysis of pulsed-SILAC quantitative proteomics data1 version - Latest release: almost 2 years ago - 3.16 thousand downloads total - 1 maintainer
BioNetStat 1.24.0 removed
Biological Network Analysis3 versions - Latest release: about 1 year ago - 9.35 thousand downloads total - 7 stars on GitHub - 1 maintainer
IsoBayes 1.2.7
IsoBayes: Single Isoform protein inference Method via Bayesian Analyses5 versions - Latest release: 9 months ago - 2.24 thousand downloads total - 7 stars on GitHub - 1 maintainer
proteasy 1.6.0 removed
Protease Mapping3 versions - Latest release: about 1 year ago - 1.34 thousand downloads total - 2 stars on GitHub - 1 maintainer
calm 1.18.0
Covariate Assisted Large-scale Multiple testing3 versions - Latest release: about 1 year ago - 5.83 thousand downloads total - 0 stars on GitHub - 1 maintainer
Related Keywords
Software
196
MassSpectrometry
92
ImmunoOncology
63
Metabolomics
53
DifferentialExpression
49
DataImport
36
Visualization
34
GeneExpression
34
QualityControl
33
Normalization
29
Clustering
29
Transcriptomics
27
Microarray
26
SystemsBiology
25
Infrastructure
25
Regression
24
Preprocessing
24
RNASeq
23
MultipleComparison
21
CellBasedAssays
19
proteomics
19
Sequencing
18
mass-spectrometry
18
Classification
16
Network
16
CellBiology
16
BiomedicalInformatics
16
Genetics
15
GeneSetEnrichment
15
SingleCell
15
r
13
TimeCourse
13
OneChannel
12
Bayesian
12
Pathways
12
bioconductor
11
Transcription
11
FeatureExtraction
10
Cheminformatics
9
Lipidomics
9
GraphAndNetwork
9
FunctionalGenomics
9
BatchEffect
8
FlowCytometry
8
metabolomics
7
StatisticalMethod
7
NetworkInference
7
mRNAMicroarray
7
TwoChannel
7
AlternativeSplicing
6
ExperimentalDesign
6
GUI
6
GO
6
Epigenetics
6
PrincipalComponent
6
ShinyApps
5
Pharmacogenomics
5
Pharmacogenetics
5
MicrotitrePlateAssay
5
KEGG
5
GenePrediction
5
rstats
5
DimensionReduction
5
DataRepresentation
5
ProprietaryPlatforms
5
Coverage
4
SNP
4
Survival
4
GeneTarget
4
bioinformatics
4
GeneSignaling
4
DifferentialSplicing
4
ExonArray
4
Reactome
4
ExperimentHubSoftware
3
WorkflowStep
3
normalization
3
GenomeWideAssociation
3
Annotation
3
Alignment
3
SequenceMatching
3
ComparativeGenomics
3
FunctionalPrediction
3
Bioinformatics
3
MicroRNAArray
3
DNAMethylation
3
proteomics-data
3
Spatial
3
PeakDetection
2
GeneRegulation
2
SomaticMutation
2
DifferentialMethylation
2
StructuralPrediction
2
genomics
2
fast
2
multiplatform
2
ResearchField
2
rpackage
2
Metagenomics
2
visualisation
2