bioc-issue-bot
commented
5 years ago Hi @ChloeHJ
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: proBatch
Type: Package
Title: Tools for Batch Effects Diagnostics and Correction
Version: 1.0.0
Author: Jelena Cuklina <chuklina.jelena@gmail.com>, Chloe H. Lee <chloe.h.lee94@gmail.com>, Patrick Pedrioli <pedrioli@gmail.com>
Maintainer: The package maintainer Jelena Cuklina <chuklina.jelena@gmail.com>
Description: The proBatch package facilitates batch effects analysis and correction
in high-thoughput experiments. Although the package has primarily been developed
for mass-spectrometry proteomics (DIA/SWATH), it should also be applicable
to most omic data with minor adaptations.
The package contains functions for diagnostics (proteome/genome-wide and feature-level),
correction (normalization and batch effects correction) and quality control.
Diagnostics part of the package features unified color scheme for plotting,
that allows to produce publication-quality graphs.
Correction functions are convenient wrappers for common normalization and
batch effects removal approaches such as quantile normalizetion and median centering.
Furthermore, the package includes non-linear fitting based approaches to deal
with complex, mass spectrometry-specific signal drifts.
Quality control step, mostly based on correlation analysis, allows to assess whether
the correction improved the quality of the data.
All steps of batch effects analysis and correction are illustrated in the vignette,
using the subset of real-world large-scale dataset.
biocViews: BatchEffect, Normalization, Preprocessing, Software, MassSpectrometry,Proteomics, QualityControl
License: GPL-3
URL: https://github.com/symbioticMe/proBatch
BugReports: https://github.com/symbioticMe/proBatch/issues
Depends: R (>= 3.5.0)
Encoding: UTF-8
LazyData: true
Imports:
Biobase,
corrplot,
dplyr,
data.table,
ggfortify,
ggplot2,
lazyeval,
lubridate,
magrittr,
pheatmap,
preprocessCore,
purrr,
pvca,
RColorBrewer,
readr,
reshape2,
rlang,
scales,
sva,
tidyr,
tidyverse,
tibble,
wesanderson,
WGCNA
Suggests: knitr,
rmarkdown
VignetteBuilder: knitr
RoxygenNote: 6.1.1
mtmorgan
Liubuntu
ChloeHJ
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