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Papers: 10.3390/biology3010085

https://doi.org/10.3390/biology3010085

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

Cited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Published: over 12 years ago

Software Mentions 28

bioconductor: AnnotationDbi
Manipulation of SQLite-based annotations in Bioconductor
Papers that mentioned: 73
Very Likely Science (90)
bioconductor: biomaRt
Interface to BioMart databases (i.e. Ensembl)
Papers that mentioned: 446
Very Likely Science (100)
bioconductor: CAMERA
Collection of annotation related methods for mass spectrometry data
Papers that mentioned: 429
Very Likely Science (75)
bioconductor: clipper
Gene Set Analysis Exploiting Pathway Topology
Papers that mentioned: 8
Very Likely Science (85)
bioconductor: DEGraph
Two-sample tests on a graph
Papers that mentioned: 15
Very Likely Science (90)
bioconductor: gaggle
Broadcast data between R and Gaggle
Papers that mentioned: 5
Very Likely Science (90)
bioconductor: graphite
GRAPH Interaction from pathway Topological Environment
Papers that mentioned: 30
Very Likely Science (100)
bioconductor: KEGGgraph
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
Papers that mentioned: 39
Very Likely Science (100)
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
Very Likely Science (78)
bioconductor: NCIgraph
Pathways from the NCI Pathways Database
Papers that mentioned: 3
Very Likely Science (100)
bioconductor: pathview
a tool set for pathway based data integration and visualization
Papers that mentioned: 144
Very Likely Science (100)
bioconductor: PSICQUIC
Papers that mentioned: 75
Unlikely Science (0)
bioconductor: rBiopaxParser
Parses BioPax files and represents them in R
Papers that mentioned: 7
Very Likely Science (100)
bioconductor: RedeR
Interactive visualization and manipulation of nested networks
Papers that mentioned: 21
Very Likely Science (100)
bioconductor: Rgraphviz
Provides plotting capabilities for R graph objects
Papers that mentioned: 33
Very Likely Science (100)
bioconductor: rsbml
R support for SBML, using libsbml
Papers that mentioned: 3
Very Likely Science (90)
bioconductor: SBMLR
SBML-R Interface and Analysis Tools
Papers that mentioned: 6
Very Likely Science (100)
bioconductor: SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Papers that mentioned: 155
Very Likely Science (100)
cran: BoolNet
Construction, Simulation and Analysis of Boolean Networks
Papers that mentioned: 73
Very Likely Science (85)
cran: CePa
Centrality-Based Pathway Enrichment
Papers that mentioned: 22
Very Likely Science (87)
cran: igraph
Network Analysis and Visualization
Papers that mentioned: 1,555
Very Likely Science (100)
cran: rJava
Low-Level R to Java Interface
Papers that mentioned: 28
Very Likely Science (75)
cran: XML
Tools for Parsing and Generating XML Within R and S-Plus
Papers that mentioned: 60
Very Likely Science (75)
pypi: clipper
A set of scripts for calling peaks on CLIP-seq data
Papers that mentioned: 8
Very Likely Science (100)
pypi: gaggle
aiohttp wrapper for google-api-client-python
Papers that mentioned: 5
Very Likely Science (65)
pypi: graphite
Papers that mentioned: 30
Very Likely Science (65)
pypi: igraph
High performance graph data structures and algorithms
Papers that mentioned: 1,555
Very Likely Science (100)
pypi: PSI
Python System Information
Papers that mentioned: 225
Very Likely Science (65)