magpie

DOI: 10.18129/B9.bioc.magpie  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see magpie.

MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	magpie Package User's Guide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DifferentialMethylation, Epitranscriptomics, RNASeq, Sequencing, Software
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.2.0)
Imports	utils, rtracklayer, Matrix, matrixStats, stats, S4Vectors, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi, aod, BiocParallel, DESeq2, openxlsx, RColorBrewer, reshape2, TRESS
LinkingTo
Suggests	knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/dxd429/magpie
BugReports	https://github.com/dxd429/magpie/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	magpie_1.0.0.tar.gz
Windows Binary	magpie_1.0.0.zip
macOS Binary (x86_64)	magpie_1.0.0.tgz
macOS Binary (arm64)	magpie_1.0.0.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