bioc-issue-bot
commented
2 years ago Hi @mrbakhsh
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: deepCE
Type: Package
Title: Inference of Interactome and Underying Protein Complexes from Co-fractionation MS Data via Deep Learning
Version: 0.99.0
Authors@R: c(
person("Matineh", "Rahmatbakhsh", ,"matinerb.94@gmail.com",c("aut","trl","cre")),
person("Mohan", "Babu", ,"mohan.babu@uregina.ca", c("led")),
person("Alla", "Gagarinova", ,"alla.gagarinova@usask.ca", c("led")))
Description: Co-fractionation mass spectrometry (CF-MS) has emerged as a powerful approach
for cell-wide identification of protein complexes that performs nearly all
biological processes and cellular activities. While computational tools based
on traditional machine learning is widely applied to analyze protein complexes,
it remains unclear if it is the most suitable choice for analyzing CF/MS
dataset. Here, we introduce deepCE, a R/Bioconductor package that employs deep
learning approaches for automated scoring of co-fractionation mass spectrometry
(CF-MS) and sophisticated clustering procedure for network inference of
underlying complexes.
Depends:
R (>= 4.1),
keras
Imports:
dplyr,
tidyr,
igraph,
ggplot2,
pROC,
PRROC,
RcppAlgos,
purrr,
tibble,
stringr,
data.table,
magrittr,
DiffCorr,
MSnbase,
stats,
grDevices,
utils
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/mrbakhsh/deepCE
BugReports: https://github.com/mrbakhsh/deepCE/issues
VignetteBuilder: knitr
Suggests:
ptw,
infotheo,
reshape2,
fmsb,
knitr,
rmarkdown,
BiocStyle,
gprofiler2,
fgsea,
lsa,
WGCNA,
plyr,
proxy,
fdrtool,
BiocGenerics,
RUnit
SystemRequirement: tensorflow
biocViews:
Proteomics,
SystemsBiology,
NetworkInference,
Network,
Clustering,
MassSpectrometry
RoxygenNote: 7.1.2
lshep
mrbakhsh
nturaga
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