bioc-issue-bot
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4 years ago Hi @cbiagii
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The DESCRIPTION file for this package is:
Package: pcitRif
Type: Package
Title: Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Version: 0.99.0
Authors@R: c(person("Carlos Alberto", "Oliveira de Biagi Junior", email = "cbiagijr@gmail.com", role = c("aut", "cre")),
person("Ricardo", "Perecin Nociti", email = "rnociti@gmail.com", role = c("aut", "ctb")),
person("Breno", "Osvaldo Funicheli", email = "osvaldobreno99@gmail.com ", role = c("aut", "ctb")),
person("João Paulo", "Bianchi Ximenez", email = "joaopaulo.ximenez@me.com", role = c("ctb")),
person("Patrícia", "de Cássia Ruy", email = "patiruy@gmail.com", role = c("ctb")),
person("Marcelo", "Gomes de Paula", email = "marcelogomesrp@gmail.com", role = c("ctb")),
person("Rafael", "dos Santos Bezerra", email = "rafaelbezerra50@yahoo.com", role = c("ctb")),
person("Wilson", "Araújo da Silva Junior", email = "wilsonjr@usp.br", role = c("aut", "ctb")))
Author: Carlos Alberto Oliveira de Biagi Jr [aut, cre], Ricardo Perecin Nociti [aut, ctb],
Breno Osvaldo Funicheli [aut, ctb], João Paulo Bianchi Ximenez [ctb],
Patrícia de Cássia Ruy [ctb], Marcelo Gomes de Paula [ctb],
Rafael dos Santos Bezerra [ctb], Wilson Araújo da Silva Junior [aut, ctb]
Description: This vignette provides the necessary instructions for performing the Partial
Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008)
and Regulatory Impact Factors (RIF) (Reverter et al. 2010) algorithm. The PCIT
algorithm identifies meaningful correlations to define edges in a weighted network
and can be applied to any correlation-based network including but not limited to
gene co-expression networks, while the RIF algorithm identify critical Transcription
Factors (TF) from gene expression data. These two algorithms when combined provide a
very relevant layer of information for gene expression studies (Microarray, RNA-seq
and single-cell RNA-seq data).
Imports: crayon, clusterProfiler, DESeq2, geomnet, GGally, ggplot2, ggpubr, graphics,
network, pbapply, reshape2, scales, stats, SummarizedExperiment, utils, dplyr, tidyr,
ggrepel
Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat
Depends: R (>= 3.6), methods
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.2
biocViews: Sequencing, RNASeq, Microarray, GeneExpression, Transcription,
Normalization, DifferentialExpression, SingleCell, Network,
Regression, ChIPSeq, ImmunoOncology, Coverage
VignetteBuilder: knitr
Maintainer: Carlos Alberto Oliveira de Biagi Junior <cbiagijr@gmail.com>
cbiagii
LiNk-NY
Kayla-Morrell
mtmorgan
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