magpie

This is the released version of magpie; for the devel version, see magpie.

MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation

Bioconductor version: Release (3.20)

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialMethylation, Epitranscriptomics, RNASeq, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.17 (R-4.3) (1.5 years)
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

Suggests	knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	magpie_1.6.0.tar.gz
Windows Binary (x86_64)	magpie_1.6.0.zip
macOS Binary (x86_64)	magpie_1.6.0.tgz
macOS Binary (arm64)	magpie_1.6.0.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