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magpie

MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation

Bioconductor version: 3.23 · Package version: 1.12.0

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.

Installation

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

BiocManager::install("magpie")

Details

MaintainerDaoyu Duan <dxd429@case.edu>
AuthorDaoyu Duan [aut, cre], Zhenxing Guo [aut]
LicenseMIT + file LICENSE
URLhttps://github.com/dxd429/magpie
Bug Reportshttps://github.com/dxd429/magpie/issues
Downloads rank422
Source branchRELEASE_3_23
biocViewsDifferentialMethylation, Epitranscriptomics, RNASeq, Sequencing, Software

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packagemagpie_1.12.0.tar.gz
Windows binary (x86_64)magpie_1.12.0.zip
macOS binary (arm64)magpie_1.12.0.tgz
macOS binary (x86_64)magpie_1.12.0.tgz
Dependencies

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

Suggests: knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle