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>
citation("magpie")):
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")| magpie Package User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialMethylation, Epitranscriptomics, RNASeq, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1 year) |
| 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 |
| System Requirements | |
| URL | https://github.com/dxd429/magpie |
| Bug Reports | https://github.com/dxd429/magpie/issues |
See More
| 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_1.0.0.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 |
| Old Source Packages for BioC 3.17 | Source Archive |