Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Papers: 10.1002/pmic.201400392
https://doi.org/10.1002/pmic.201400392
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Published: about 9 years ago
Software Mentions 62
bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSetPapers that mentioned: 1,962
bioconductor: BRAIN
Baffling Recursive Algorithm for Isotope distributioN calculationsPapers that mentioned: 10
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distributionPapers that mentioned: 9,583
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in RPapers that mentioned: 6,568
bioconductor: gage
Generally Applicable Gene-set Enrichment for Pathway AnalysisPapers that mentioned: 45
bioconductor: Gviz
Plotting data and annotation information along genomic coordinatesPapers that mentioned: 134
bioconductor: interactiveDisplay
Package for enabling powerful shiny web displays of Bioconductor objectsPapers that mentioned: 1
bioconductor: isobar
Analysis and quantitation of isobarically tagged MSMS proteomics dataPapers that mentioned: 4
bioconductor: marray
Exploratory analysis for two-color spotted microarray dataPapers that mentioned: 62
bioconductor: MassSpecWavelet
Peak Detection for Mass Spectrometry data using wavelet-based algorithmsPapers that mentioned: 19
bioconductor: MSGFgui
Papers that mentioned: 1bioconductor: msmsEDA
Exploratory Data Analysis of LC-MS/MS data by spectral countsPapers that mentioned: 2
bioconductor: MSnbase
Base Functions and Classes for Mass Spectrometry and ProteomicsPapers that mentioned: 24
bioconductor: MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics ExperimentsPapers that mentioned: 115
bioconductor: mzR
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)Papers that mentioned: 12
bioconductor: pRoloc
A unifying bioinformatics framework for spatial proteomicsPapers that mentioned: 12
bioconductor: pRolocGUI
Interactive visualisation of spatial proteomics dataPapers that mentioned: 5
bioconductor: PSICQUIC
Papers that mentioned: 75bioconductor: Rgraphviz
Provides plotting capabilities for R graph objectsPapers that mentioned: 33
bioconductor: RNAinteract
Estimate Pairwise Interactions from multidimensional featuresPapers that mentioned: 1
bioconductor: SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsPapers that mentioned: 155
cran: FactoMineR
Multivariate Exploratory Data Analysis and Data MiningPapers that mentioned: 1,101
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of GraphicsPapers that mentioned: 11,441
cran: protViz
Visualizing and Analyzing Mass Spectrometry Related Data in ProteomicsPapers that mentioned: 4
pypi: fasta
The fasta python package enables you to deal with biological sequence files easily.Papers that mentioned: 848
pypi: lattice
A framework for developing data models, including schema development and documentation.Papers that mentioned: 251
pypi: xcms
calculated extended contact mode score provided the query and template protein-ligand structuresPapers that mentioned: 68