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magpie

This is the development version of magpie; for the stable release version, see magpie.

MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation


Bioconductor version: Development (3.19)

This package aims to perform power analysis for the MeRIP-seq study. It calculates FDR, FDC, power, and precision under various study design parameters, including but not limited to sample size, sequencing depth, and testing method. It can also output results into .xlsx files or produce corresponding figures of choice.

Author: Daoyu Duan [aut, cre], Zhenxing Guo [aut]

Maintainer: Daoyu Duan <dxd429 at case.edu>

Citation (from within R, enter citation("magpie")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("magpie")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("magpie")
magpie Package User's Guide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialMethylation, Epitranscriptomics, RNASeq, Sequencing, Software
Version 1.3.1
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License MIT + file LICENSE
Depends R (>= 4.3.0)
Imports utils, rtracklayer, Matrix, matrixStats, stats, S4Vectors, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi, aod, BiocParallel, DESeq2, openxlsx, RColorBrewer, reshape2, TRESS
System Requirements
URL https://github.com/dxd429/magpie
Bug Reports https://github.com/dxd429/magpie/issues
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Suggests knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package magpie_1.3.1.tar.gz
Windows Binary magpie_1.3.1.zip
macOS Binary (x86_64) magpie_1.3.1.tgz
macOS Binary (arm64) magpie_1.3.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/magpie
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/magpie
Bioc Package Browser https://code.bioconductor.org/browse/magpie/
Package Short Url https://bioconductor.org/packages/magpie/
Package Downloads Report Download Stats