Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "Proteomics" keyword
Top 0.3% on bioconductor.org
5 versions - Latest release: 20 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
limma 3.60.0
Linear Models for Microarray Data5 versions - Latest release: 20 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
MsQuality 1.2.1
MsQuality - Quality metric calculation from Spectra and MsExperiment objects4 versions - Latest release: 2 months ago - 1.6 thousand downloads total - 7 stars on GitHub - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data4 versions - Latest release: 16 days ago - 3.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
Cardinal 3.4.3
A mass spectrometry imaging toolbox for statistical analysis4 versions - Latest release: 5 months ago - 26.1 thousand downloads total - 1 maintainer
MsBackendMgf 1.10.0
Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files3 versions - Latest release: 6 months ago - 3 dependent packages - 22 thousand downloads total - 4 stars on GitHub - 2 maintainers
infinityFlow 1.12.0
Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions3 versions - Latest release: 6 months ago - 4.46 thousand downloads total - 1 maintainer
vsclust 1.4.0
Feature-based variance-sensitive quantitative clustering3 versions - Latest release: 6 months ago - 1.7 thousand downloads total - 1 maintainer
cisPath 1.42.0
Visualization and management of the protein-protein interaction networks.3 versions - Latest release: 6 months ago - 21.2 thousand downloads total - 1 maintainer
Top 5.0% on bioconductor.org
4 versions - Latest release: 5 months ago - 19 dependent packages - 157 thousand downloads total - 16 stars on GitHub - 1 maintainer
MsCoreUtils 1.14.1
Core Utils for Mass Spectrometry Data4 versions - Latest release: 5 months ago - 19 dependent packages - 157 thousand downloads total - 16 stars on GitHub - 1 maintainer
artMS 1.20.0
Analytical R tools for Mass Spectrometry3 versions - Latest release: 6 months ago - 9.23 thousand downloads total - 1 maintainer
Top 8.6% on bioconductor.org
4 versions - Latest release: 15 days ago - 15 dependent packages - 47.5 thousand downloads total - 31 stars on GitHub - 1 maintainer
Spectra 1.14.0
Spectra Infrastructure for Mass Spectrometry Data4 versions - Latest release: 15 days ago - 15 dependent packages - 47.5 thousand downloads total - 31 stars on GitHub - 1 maintainer
Rtpca 1.12.0
Thermal proximity co-aggregation with R3 versions - Latest release: 6 months ago - 3.54 thousand downloads total - 1 maintainer
TargetDecoy 1.8.0
Diagnostic Plots to Evaluate the Target Decoy Approach3 versions - Latest release: 6 months ago - 2.39 thousand downloads total - 0 stars on GitHub - 1 maintainer
NanoStringNCTools 1.10.1
NanoString nCounter Tools4 versions - Latest release: about 1 month ago - 2 dependent packages - 14.3 thousand downloads total - 1 maintainer
Top 7.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 34.1 thousand downloads total - 1 maintainer
plgem 1.74.0
Detect differential expression in microarray and proteomics datasets with the Power Law Global Er...3 versions - Latest release: 6 months ago - 1 dependent package - 34.1 thousand downloads total - 1 maintainer
SpacePAC 1.40.0
Identification of Mutational Clusters in 3D Protein Space via Simulation.3 versions - Latest release: 6 months ago - 1 dependent package - 18.2 thousand downloads total - 1 maintainer
MQmetrics 1.10.0
Quality Control of Protemics Data3 versions - Latest release: 6 months ago - 2.66 thousand downloads total - 1 maintainer
wpm 1.12.0
Well Plate Maker3 versions - Latest release: 6 months ago - 4 thousand downloads total - 5 stars on GitHub - 1 maintainer
cydar 1.26.0
Using Mass Cytometry for Differential Abundance Analyses3 versions - Latest release: 6 months ago - 13.2 thousand downloads total - 1 maintainer
specL 1.36.0
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics3 versions - Latest release: 6 months ago - 15.8 thousand downloads total - 1 maintainer
rScudo 1.18.1
Signature-based Clustering for Diagnostic Purposes4 versions - Latest release: 3 months ago - 5.75 thousand downloads total - 3 stars on GitHub - 1 maintainer
RCASPAR 1.48.0
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.3 versions - Latest release: 6 months ago - 21.4 thousand downloads total - 2 maintainers
sparsenetgls 1.20.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...3 versions - Latest release: 6 months ago - 5.7 thousand downloads total - 1 maintainer
MSstatsQCgui 1.22.0
A graphical user interface for MSstatsQC package3 versions - Latest release: 6 months ago - 6.85 thousand downloads total - 1 maintainer
CONSTANd 1.10.0
Data normalization by matrix raking3 versions - Latest release: 6 months ago - 3.41 thousand downloads total - 1 maintainer
Path2PPI 1.32.0
Prediction of pathway-related protein-protein interaction networks3 versions - Latest release: 6 months ago - 12.6 thousand downloads total - 1 maintainer
phenomis 1.4.0
Postprocessing and univariate analysis of omics data3 versions - Latest release: 6 months ago - 1.98 thousand downloads total - 1 maintainer
MBQN 2.14.0
Mean/Median-balanced quantile normalization3 versions - Latest release: 6 months ago - 4.27 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 33 thousand downloads total - 1 maintainer
MSnID 1.36.0
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications3 versions - Latest release: 6 months ago - 33 thousand downloads total - 1 maintainer
MSstatsQC 2.20.0
Longitudinal system suitability monitoring and quality control for proteomic experiments3 versions - Latest release: 6 months ago - 1 dependent package - 9.18 thousand downloads total - 1 maintainer
ASEB 1.46.3
Predict Acetylated Lysine Sites3 versions - Latest release: 6 months ago - 24.5 thousand downloads total - 1 maintainer
MSstatsTMT 2.10.0
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tande...3 versions - Latest release: 6 months ago - 2 dependent packages - 17 thousand downloads total - 1 maintainer
deltaGseg 1.42.0
deltaGseg3 versions - Latest release: 6 months ago - 19.2 thousand downloads total - 1 maintainer
PhosR 1.12.0
A set of methods and tools for comprehensive analysis of phosphoproteomics data3 versions - Latest release: 6 months ago - 5.6 thousand downloads total - 1 maintainer
diffuStats 1.22.0
Diffusion scores on biological networks3 versions - Latest release: 6 months ago - 9.33 thousand downloads total - 1 maintainer
CNORdt 1.44.0
Add-on to CellNOptR: Discretized time treatments3 versions - Latest release: 6 months ago - 21.7 thousand downloads total - 1 maintainer
ROTS 1.30.0
Reproducibility-Optimized Test Statistic3 versions - Latest release: 6 months ago - 2 dependent packages - 23.4 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
2 versions - Latest release: 6 months 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: 6 months ago - 26.7 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 2 dependent packages - 35.1 thousand downloads total - 1 maintainer
BRAIN 1.48.0
Baffling Recursive Algorithm for Isotope distributioN calculations3 versions - Latest release: 6 months ago - 2 dependent packages - 35.1 thousand downloads total - 1 maintainer
PECA 1.38.0
Probe-level Expression Change Averaging3 versions - Latest release: 6 months ago - 1 dependent package - 17.8 thousand downloads total - 1 maintainer
pgca 1.26.0
PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data3 versions - Latest release: 6 months ago - 8.19 thousand downloads total - 1 maintainer
PrInCE 1.18.0
Predicting Interactomes from Co-Elution3 versions - Latest release: 6 months ago - 5.92 thousand downloads total - 6 stars on GitHub - 1 maintainer
SpatialOmicsOverlay 1.2.1
Spatial Overlay for Omic Data from Nanostring GeoMx Data3 versions - Latest release: 6 months ago - 1.68 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 33.6 thousand downloads total - 1 maintainer
msmsTests 1.40.0
LC-MS/MS Differential Expression Tests3 versions - Latest release: 6 months ago - 1 dependent package - 33.6 thousand downloads total - 1 maintainer
proBAMr 1.36.0
Generating SAM file for PSMs in shotgun proteomics data3 versions - Latest release: 6 months ago - 15.3 thousand downloads total - 1 maintainer
IMMAN 1.22.0
Interlog protein network reconstruction by Mapping and Mining ANalysis3 versions - Latest release: 6 months ago - 7.17 thousand downloads total - 1 maintainer
Top 6.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 51.2 thousand downloads total - 1 maintainer
hpar 1.44.0
Human Protein Atlas in R3 versions - Latest release: 6 months ago - 3 dependent packages - 51.2 thousand downloads total - 1 maintainer
MsDataHub 1.2.0
Mass Spectrometry Data on ExperimentHub3 versions - Latest release: 6 months ago - 2 dependent packages - 1.52 thousand downloads total - 1 stars on GitHub - 1 maintainer
GenProSeq 1.6.0
Generating Protein Sequences with Deep Generative Models3 versions - Latest release: 6 months ago - 1.81 thousand downloads total - 1 maintainer
synapter 2.26.0
Label-free data analysis pipeline for optimal identification and quantitation3 versions - Latest release: 6 months ago - 29.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
MSstatsConvert 1.12.1
Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format4 versions - Latest release: 2 months ago - 6 dependent packages - 18.6 thousand downloads total - 1 maintainer
Top 6.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 45.4 thousand downloads total - 1 maintainer
DEP 1.24.0
Differential Enrichment analysis of Proteomics data3 versions - Latest release: 6 months ago - 1 dependent package - 45.4 thousand downloads total - 1 maintainer
Prostar 1.34.6
Provides a GUI for DAPAR6 versions - Latest release: 3 months ago - 17.8 thousand downloads total - 1 maintainer
MatrixQCvis 1.10.0
Shiny-based interactive data-quality exploration for omics data3 versions - Latest release: 6 months ago - 4.12 thousand downloads total - 1 maintainer
customProDB 1.42.1
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics ...4 versions - Latest release: 2 months ago - 26 thousand downloads total - 1 maintainer
phosphonormalizer 1.26.0
Compensates for the bias introduced by median normalization in3 versions - Latest release: 6 months ago - 9.22 thousand downloads total - 1 maintainer
Pviz 1.36.0
Peptide Annotation and Data Visualization using Gviz3 versions - Latest release: 6 months ago - 1 dependent package - 16.8 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 6 dependent packages - 37.4 thousand downloads total - 1 maintainer
CellNOptR 1.48.0
Training of boolean logic models of signalling networks using prior knowledge networks and pertur...3 versions - Latest release: 6 months ago - 6 dependent packages - 37.4 thousand downloads total - 1 maintainer
cytoKernel 1.8.0
Differential expression using kernel-based score test3 versions - Latest release: 6 months ago - 2.32 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 7.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 33.5 thousand downloads total - 1 maintainer
Rcpi 1.38.0
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery3 versions - Latest release: 6 months ago - 1 dependent package - 33.5 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 29.4 thousand downloads total - 1 maintainer
procoil 2.30.0
Prediction of Oligomerization of Coiled Coil Proteins3 versions - Latest release: 6 months ago - 29.4 thousand downloads total - 1 maintainer
DAPAR 1.34.6
Tools for the Differential Analysis of Proteins Abundance with R6 versions - Latest release: 3 months ago - 1 dependent package - 20.5 thousand downloads total - 1 maintainer
NPARC 1.14.0
Non-parametric analysis of response curves for thermal proteome profiling experiments3 versions - Latest release: 6 months ago - 4.98 thousand downloads total - 1 maintainer
PAA 1.36.0
PAA (Protein Array Analyzer)3 versions - Latest release: 6 months ago - 17.6 thousand downloads total - 2 maintainers
CausalR 1.34.0
Causal network analysis methods3 versions - Latest release: 6 months ago - 13.2 thousand downloads total - 2 maintainers
Top 7.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 2 dependent packages - 34.3 thousand downloads total - 1 maintainer
msmsEDA 1.40.0
Exploratory Data Analysis of LC-MS/MS data by spectral counts3 versions - Latest release: 6 months ago - 2 dependent packages - 34.3 thousand downloads total - 1 maintainer
ComPrAn 1.10.0
Complexome Profiling Analysis package3 versions - Latest release: 6 months ago - 2.84 thousand downloads total - 1 maintainer
bandle 1.6.0
An R package for the Bayesian analysis of differential subcellular localisation experiments3 versions - Latest release: 6 months ago - 2.26 thousand downloads total - 5 stars on GitHub - 1 maintainer
iPAC 1.46.0
Identification of Protein Amino acid Clustering3 versions - Latest release: 6 months ago - 3 dependent packages - 23.5 thousand downloads total - 1 maintainer
Top 8.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 28.4 thousand downloads total - 1 maintainer
PLPE 1.62.0
Local Pooled Error Test for Differential Expression with Paired High-throughput Data3 versions - Latest release: 6 months ago - 28.4 thousand downloads total - 1 maintainer
pepXMLTab 1.36.0
Parsing pepXML files and filter based on peptide FDR.3 versions - Latest release: 6 months ago - 14.8 thousand downloads total - 1 maintainer
clippda 1.52.0
A package for the clinical proteomic profiling data analysis3 versions - Latest release: 6 months ago - 27.7 thousand downloads total - 1 maintainer
XINA 1.20.0
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis3 versions - Latest release: 6 months ago - 6.4 thousand downloads total - 1 maintainer
DIAlignR 2.10.0
Dynamic Programming Based Alignment of MS2 Chromatograms3 versions - Latest release: 6 months ago - 4.83 thousand downloads total - 6 stars on GitHub - 1 maintainer
CNORode 1.44.0
ODE add-on to CellNOptR3 versions - Latest release: 6 months ago - 1 dependent package - 26.9 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 51.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
fmcsR 1.44.0
Mismatch Tolerant Maximum Common Substructure Searching3 versions - Latest release: 6 months ago - 1 dependent package - 51.3 thousand downloads total - 5 stars on GitHub - 1 maintainer
QuartPAC 1.34.0
Identification of mutational clusters in protein quaternary structures3 versions - Latest release: 6 months ago - 12.5 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
4 versions - Latest release: 4 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
EGSEA 1.30.1
Ensemble of Gene Set Enrichment Analyses4 versions - Latest release: 4 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
deco 1.18.0 removed
Decomposing Heterogeneous Cohorts using Omic Data Profiling2 versions - Latest release: 6 months ago - 4.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
DominoEffect 1.22.0
Identification and Annotation of Protein Hotspot Residues3 versions - Latest release: 6 months ago - 7.57 thousand downloads total - 2 maintainers
PSMatch 1.6.0
Handling and Managing Peptide Spectrum Matches3 versions - Latest release: 6 months ago - 2 dependent packages - 6.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
ProteoMM 1.20.0
Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform3 versions - Latest release: 6 months ago - 7.59 thousand downloads total - 1 maintainer
omicRexposome 1.24.3
Exposome and omic data associatin and integration analysis4 versions - Latest release: 3 months ago - 7.99 thousand downloads total - 1 maintainer
SDAMS 1.22.0
Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequen...3 versions - Latest release: 6 months ago - 7.52 thousand downloads total - 1 maintainer
GeomxTools 3.6.2
NanoString GeoMx Tools4 versions - Latest release: 3 months ago - 3 dependent packages - 15.9 thousand downloads total - 1 maintainer
biosigner 1.30.0
Signature discovery from omics data3 versions - Latest release: 6 months ago - 2 dependent packages - 14.2 thousand downloads total - 1 maintainer
SMAD 1.18.0
Statistical Modelling of AP-MS Data (SMAD)3 versions - Latest release: 6 months ago - 5.26 thousand downloads total - 1 maintainer
MSstatsLOBD 1.10.0
Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)3 versions - Latest release: 6 months ago - 2.85 thousand downloads total - 0 stars on GitHub - 1 maintainer
TPP 3.30.0
Analyze thermal proteome profiling (TPP) experiments3 versions - Latest release: 6 months ago - 1 dependent package - 19.1 thousand downloads total - 1 maintainer
ProteoDisco 1.8.0
Generation of customized protein variant databases from genomic variants, splice-junctions and ma...3 versions - Latest release: 6 months ago - 2.49 thousand downloads total - 4 stars on GitHub - 1 maintainer
GraphPAC 1.44.0
Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.3 versions - Latest release: 6 months ago - 1 dependent package - 20.8 thousand downloads total - 1 maintainer
idpr 1.12.0
Profiling and Analyzing Intrinsically Disordered Proteins in R3 versions - Latest release: 6 months ago - 4.08 thousand downloads total - 4 stars on GitHub - 1 maintainer
rain 1.36.0
Rhythmicity Analysis Incorporating Non-parametric Methods3 versions - Latest release: 6 months ago - 19.2 thousand downloads total - 1 maintainer
KinSwingR 1.20.0
KinSwingR: network-based kinase activity prediction3 versions - Latest release: 6 months ago - 6.07 thousand downloads total - 1 maintainer
AssessORF 1.20.0
Assess Gene Predictions Using Proteomics and Evolutionary Conservation3 versions - Latest release: 6 months ago - 6.79 thousand downloads total - 1 maintainer
phemd 1.18.0
Phenotypic EMD for comparison of single-cell samples3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
Doscheda 1.24.0
A DownStream Chemo-Proteomics Analysis Pipeline3 versions - Latest release: 6 months ago - 8.5 thousand downloads total - 1 maintainer
fCI 1.32.0
f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics3 versions - Latest release: 6 months ago - 11.9 thousand downloads total - 1 maintainer
HPiP 1.8.0
Host-Pathogen Interaction Prediction3 versions - Latest release: 6 months ago - 2.55 thousand downloads total - 3 stars on GitHub - 1 maintainer
CNORfeeder 1.42.0
Integration of CellNOptR to add missing links3 versions - Latest release: 6 months ago - 21.5 thousand downloads total - 1 maintainer
Related Keywords
Software
179
MassSpectrometry
82
ImmunoOncology
60
Metabolomics
47
DifferentialExpression
42
DataImport
33
Visualization
31
GeneExpression
31
QualityControl
30
Normalization
27
Clustering
27
Microarray
25
SystemsBiology
24
Transcriptomics
23
Infrastructure
22
MultipleComparison
20
RNASeq
20
Regression
20
Preprocessing
19
CellBasedAssays
19
Sequencing
17
proteomics
16
mass-spectrometry
15
Classification
15
BiomedicalInformatics
15
CellBiology
15
Genetics
14
GeneSetEnrichment
14
SingleCell
14
Network
14
r
12
TimeCourse
12
OneChannel
12
bioconductor
11
Transcription
10
Pathways
10
Bayesian
10
Cheminformatics
9
GraphAndNetwork
9
Lipidomics
8
FlowCytometry
8
FunctionalGenomics
8
FeatureExtraction
8
StatisticalMethod
7
TwoChannel
7
BatchEffect
7
GUI
6
ExperimentalDesign
6
NetworkInference
6
metabolomics
6
mRNAMicroarray
6
DataRepresentation
5
GO
5
MicrotitrePlateAssay
5
Pharmacogenetics
5
Pharmacogenomics
5
GenePrediction
5
rstats
5
ProprietaryPlatforms
5
AlternativeSplicing
5
PrincipalComponent
5
DimensionReduction
5
Epigenetics
5
Survival
4
Reactome
4
SNP
4
KEGG
4
GeneSignaling
4
GeneTarget
4
ExonArray
4
MicroRNAArray
3
ShinyApps
3
FunctionalPrediction
3
Bioinformatics
3
DifferentialSplicing
3
ExperimentHubSoftware
3
SequenceMatching
3
Alignment
3
WorkflowStep
3
GenomeWideAssociation
3
ComparativeGenomics
3
bioinformatics
3
Coverage
3
proteomics-data
3
Annotation
3
single-cell
2
Metagenomics
2
PeakDetection
2
StructuralPrediction
2
visualisation
2
transcriptomics
2
GeneRegulation
2
SomaticMutation
2
GenomeAnnotation
2
data
2
Spatial
2
ResearchField
2
DNAMethylation
2
CopyNumberVariation
2
normalization
2