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

Visualization of proteomics data using R and Bioconductor

Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Published: over 9 years ago

Software Mentions 62

bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Papers that mentioned: 1,962
bioconductor: biomaRt
Interface to BioMart databases (i.e. Ensembl)
Papers that mentioned: 446
bioconductor: BRAIN
Baffling Recursive Algorithm for Isotope distributioN calculations
Papers that mentioned: 10
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
bioconductor: gage
Generally Applicable Gene-set Enrichment for Pathway Analysis
Papers that mentioned: 45
bioconductor: GEOquery
Get data from NCBI Gene Expression Omnibus (GEO)
Papers that mentioned: 328
bioconductor: ggbio
Visualization tools for genomic data
Papers that mentioned: 53
bioconductor: GOstats
Tools for manipulating GO and microarrays
Papers that mentioned: 368
bioconductor: graph
graph: A package to handle graph data structures
Papers that mentioned: 45
bioconductor: Gviz
Plotting data and annotation information along genomic coordinates
Papers that mentioned: 134
bioconductor: hpar
Human Protein Atlas in R
Papers that mentioned: 5
bioconductor: interactiveDisplay
Package for enabling powerful shiny web displays of Bioconductor objects
Papers that mentioned: 1
bioconductor: isobar
Analysis and quantitation of isobarically tagged MSMS proteomics data
Papers that mentioned: 4
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: marray
Exploratory analysis for two-color spotted microarray data
Papers that mentioned: 62
bioconductor: MassSpecWavelet
Peak Detection for Mass Spectrometry data using wavelet-based algorithms
Papers that mentioned: 19
bioconductor: Mfuzz
Soft clustering of time series gene expression data
Papers that mentioned: 160
bioconductor: MSGFgui
Papers that mentioned: 1
bioconductor: msmsEDA
Exploratory Data Analysis of LC-MS/MS data by spectral counts
Papers that mentioned: 2
bioconductor: msmsTests
LC-MS/MS Differential Expression Tests
Papers that mentioned: 4
bioconductor: MSnbase
Base Functions and Classes for Mass Spectrometry and Proteomics
Papers that mentioned: 24
bioconductor: MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Papers that mentioned: 115
bioconductor: mzR
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
Papers that mentioned: 12
bioconductor: PAA
PAA (Protein Array Analyzer)
Papers that mentioned: 19
bioconductor: PROcess
Ciphergen SELDI-TOF Processing
Papers that mentioned: 15
bioconductor: pRoloc
A unifying bioinformatics framework for spatial proteomics
Papers that mentioned: 12
bioconductor: pRolocGUI
Interactive visualisation of spatial proteomics data
Papers that mentioned: 5
bioconductor: PSICQUIC
Papers that mentioned: 75
bioconductor: Pviz
Peptide Annotation and Data Visualization using Gviz
Papers that mentioned: 3
bioconductor: qcmetrics
A Framework for Quality Control
Papers that mentioned: 1
bioconductor: RBGL
An interface to the BOOST graph library
Papers that mentioned: 18
bioconductor: Rgraphviz
Provides plotting capabilities for R graph objects
Papers that mentioned: 33
bioconductor: RNAinteract
Estimate Pairwise Interactions from multidimensional features
Papers that mentioned: 1
bioconductor: rpx
R Interface to the ProteomeXchange Repository
Papers that mentioned: 1
bioconductor: SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Papers that mentioned: 155
bioconductor: SRAdb
A compilation of metadata from NCBI SRA and tools
Papers that mentioned: 20
bioconductor: UniProt.ws
R Interface to UniProt Web Services
Papers that mentioned: 10
bioconductor: xcms
LC-MS and GC-MS Data Analysis
Papers that mentioned: 68
cran: corrplot
Visualization of a Correlation Matrix
Papers that mentioned: 1,077
cran: dendextend
Extending 'dendrogram' Functionality in R
Papers that mentioned: 201
cran: FactoMineR
Multivariate Exploratory Data Analysis and Data Mining
Papers that mentioned: 1,101
cran: fasta
Fast Adaptive Shrinkage/Thresholding Algorithm
Papers that mentioned: 848
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
cran: ggvis
Interactive Grammar of Graphics
Papers that mentioned: 7
cran: gplots
Various R Programming Tools for Plotting Data
Papers that mentioned: 2,122
cran: igraph
Network Analysis and Visualization
Papers that mentioned: 1,555
cran: knitr
A General-Purpose Package for Dynamic Report Generation in R
Papers that mentioned: 157
cran: lattice
Trellis Graphics for R
Papers that mentioned: 251
cran: MALDIquant
Quantitative Analysis of Mass Spectrometry Data
Papers that mentioned: 74
cran: protViz
Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Papers that mentioned: 4
cran: RColorBrewer
ColorBrewer Palettes
Papers that mentioned: 490
cran: rgl
3D Visualization Using OpenGL
Papers that mentioned: 156
cran: VennDiagram
Generate High-Resolution Venn and Euler Plots
Papers that mentioned: 626
pypi: fasta
The fasta python package enables you to deal with biological sequence files easily.
Papers that mentioned: 848
pypi: graph
Directed and undirected graph data structures and algorithms.
Papers that mentioned: 45
pypi: igraph
High performance graph data structures and algorithms
Papers that mentioned: 1,555
pypi: isobar
A Python library to express and manipulate musical patterns
Papers that mentioned: 4
pypi: lattice
A framework for developing data models, including schema development and documentation.
Papers that mentioned: 251
pypi: pca
pca: A Python Package for Principal Component Analysis.
Papers that mentioned: 60
pypi: stats
Calculator-style statistical functions
Papers that mentioned: 3,105
pypi: xcms
calculated extended contact mode score provided the query and template protein-ligand structures
Papers that mentioned: 68