bioc-issue-bot
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3 years ago Hi @marouenbg
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The DESCRIPTION file for this package is:
Package: netZooR
Title: Integrate methods: PANDA, LIONESS, CONDOR, ALPACA, SAMBAR, MONSTER and OTTER into one workflow
Version: 0.99.1
Date: 2020-11-20
Authors@R: c(person("Tian", "Wang",
email = "twang@hsph.harvard.edu", role = c("aut", "cre")),
person("Marouen", "Ben Guebila",
email = "benguebila@hsph.harvard.edu", role = c("aut","ctb")),
person("John", "Platig",
email="john.platig@channing.harvard.edu",role="aut"),
person("Marieke", "Kuijjer",
email = "marieke.kuijjer@ncmm.uio.no", role = "aut"),
person("Magha", "Padi",
email = "mpadi@email.arizona.edu", role = "aut"),
person("Rebekka", "Burkholz",
email = "rburkholz@hsph.harvard.edu",role = "aut"),
person("Deborah", "Weighill",
email = "",role = "aut"))
Description: PANDA(Passing Attributes between Networks for Data Assimilation) is a message-passing model to reconstruction gene regulatory network. It integrates multiple sources of biological data, including protein-protein interaction data, gene expression data, and sequence motif information to reconstruct genome-wide, condition-specific regulatory networks.[(Glass et al. 2013)]. LIONESS(Linear Interpolation to Obtain Network Estimates for Single Samples) is a method to estimate sample-specific regulatory networks by applying linear interpolation to the predictions made by existing aggregate network inference approaches. CONDOR(COmplex Network Description Of Regulators)is a bipartite community structure analysis tool of biological networks, especially eQTL networks, including a method for scoring nodes based on their modularity contribution.[(Platig et al. 2016). ALPACA(ALtered Partitions Across Community Architectures) is a method for comparing two genome-scale networks derived from different phenotypic states to identify condition-specific modules.[(Padi and Quackenbush 2018)]. This package integrates pypanda--the Python implementation of PANDA and LIONESS(https://github.com/davidvi/pypanda),the R implementation of CONDOR(https://github.com/jplatig/condor) and the R implementation of ALPACA (https://github.com/meghapadi/ALPACA) into one workflow. Each tool can be call in this package by one function, and the relevant output could be accessible in current R session for downstream analysis.
Depends: R (>= 3.3),
igraph,
reticulate,
pandaR,
biocViews:
Imports: RCy3,
viridisLite,
STRINGdb,
Biobase,
matrixStats,
GOstats,
GO.db,
org.Hs.eg.db,
Matrix,
gplots,
nnet,
data.table,
vegan,
stats,
utils,
reshape,
reshape2,
penalized,
parallel,
doParallel,
foreach,
ggplot2,
ggdendro,
grid,
MASS,
assertthat,
tidyr,
methods,
AnnotationDbi,
dplyr,
IRanges,
GenomicRanges,
Remotes: jnpaulson/pandaR,
PadiLab/CRANE,
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests:
testthat (>= 2.1.0),
knitr,
rmarkdown,
pkgdown,
VignetteBuilder: knitr
RoxygenNote: 7.1.1
lshep
rohanbiju
marouenbg
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