magpie

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see magpie.

MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation

Bioconductor version: 3.21

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 "4.5") 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 1.8.0

In Bioconductor since BioC 3.17 (R-4.3) (2.5 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

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Package Archives

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

Source Package magpie_1.8.0.tar.gz

Windows Binary (x86_64) magpie_1.8.0.zip

macOS Binary (x86_64) magpie_1.8.0.tgz

macOS Binary (arm64) magpie_1.8.0.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/

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