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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/magpie.html below:

Bioconductor - magpie (development version)

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 (3.22)

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")

# 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")
Details biocViews DifferentialMethylation, Epitranscriptomics, RNASeq, Sequencing, Software Version 1.9.0 In Bioconductor since BioC 3.17 (R-4.3) (2 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 See More Package Archives

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

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