Papers: 10.1371/journal.pcbi.1007792

https://doi.org/10.1371/journal.pcbi.1007792

eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research

Cited by: 38
Author(s): Augusto Anguita‐Ruiz, Alberto Segura‐Delgado, Rafael Alcalá, Concepción M. Aguilera, Jesús Alcalá‐Fdez
Published: over 6 years ago

Software Mentions 23

bioconductor: affy
Methods for Affymetrix Oligonucleotide Arrays
Papers that mentioned: 989
Very Likely Science (98)
bioconductor: affyPLM
Methods for fitting probe-level models
Papers that mentioned: 162
Very Likely Science (100)
bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
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Very Likely Science (83)
bioconductor: Biobase
Biobase: Base functions for Bioconductor
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Very Likely Science (75)
bioconductor: Biostrings
Efficient manipulation of biological strings
Papers that mentioned: 220
Very Likely Science (65)
bioconductor: FGNet
Functional Gene Networks derived from biological enrichment analyses
Papers that mentioned: 7
Very Likely Science (100)
bioconductor: genefilter
genefilter: methods for filtering genes from high-throughput experiments
Papers that mentioned: 142
Very Likely Science (75)
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
Very Likely Science (78)
bioconductor: oligo
Preprocessing tools for oligonucleotide arrays
Papers that mentioned: 204
Very Likely Science (90)
bioconductor: topGO
Enrichment Analysis for Gene Ontology
Papers that mentioned: 652
Very Likely Science (100)
cran: arules
Mining Association Rules and Frequent Itemsets
Papers that mentioned: 42
Very Likely Science (100)
cran: arulesViz
Visualizing Association Rules and Frequent Itemsets
Papers that mentioned: 11
Very Likely Science (100)
cran: dplyr
A Grammar of Data Manipulation
Papers that mentioned: 1,213
Very Likely Science (100)
cran: fdrtool
Estimation of (Local) False Discovery Rates and Higher Criticism
Papers that mentioned: 124
Very Likely Science (80)
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
Very Likely Science (100)
cran: lattice
Trellis Graphics for R
Papers that mentioned: 251
Very Likely Science (85)
cran: Matrix
Sparse and Dense Matrix Classes and Methods
Papers that mentioned: 172
Very Likely Science (75)
cran: rpart
Recursive Partitioning and Regression Trees
Papers that mentioned: 431
Very Likely Science (100)
pypi: arules
multi-purpose association rules analysis
Papers that mentioned: 42
Very Likely Science (75)
pypi: Biology
Biological Analysis
Papers that mentioned: 311
Very Likely Science (90)
pypi: lattice
A framework for developing data models, including schema development and documentation.
Papers that mentioned: 251
Very Likely Science (80)
pypi: oligo
UNOFFICIAL Python client for i-DE
Papers that mentioned: 204
Very Likely Science (65)
pypi: PACE
Data Quality of Experimental Data
Papers that mentioned: 13,779
Very Likely Science (90)