Package: magpie 1.13.0

Daoyu Duan

magpie: MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation

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.

Authors:Daoyu Duan [aut, cre], Zhenxing Guo [aut]

magpie_1.13.0.tar.gz
magpie_1.13.0.zip(r-4.7)magpie_1.13.0.zip(r-4.6)magpie_1.13.0.zip(r-4.5)
magpie_1.13.0.tgz(r-4.6-any)magpie_1.13.0.tgz(r-4.5-any)
magpie_1.13.0.tar.gz(r-4.7-any)magpie_1.13.0.tar.gz(r-4.6-any)
magpie_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
magpie/json (API)

# Install 'magpie' in R:

install.packages('magpie', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dxd429/magpie/issues

Datasets:

power.test - Power calculation results for GSE46705
power.test - Power calculation results for GSE46705
power.test - Power calculation results for GSE46705
power.test - Power calculation results for GSE46705
power.test - Power calculation results for GSE46705
power.test - Power calculation results for GSE46705

On BioConductor:magpie-1.13.0(bioc 3.24)magpie-1.12.0(bioc 3.23)

epitranscriptomics differentialmethylation sequencing rnaseq software

4.61 score 41 scripts 316 downloads 8 exports 90 dependencies

Last updated from:08d47729a7. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	255
linux-devel-x86_64	WARNING	452
source / vignettes	OK	309
linux-release-x86_64	WARNING	444
macos-release-arm64	WARNING	193
macos-oldrel-arm64	WARNING	198
windows-devel	WARNING	302
windows-release	WARNING	331
windows-oldrel	WARNING	306
wasm-release	OK	229

Exports:plotAll plotAll_Strata plotRes plotStrata powerEval quickPower writeToxlsx writeToxlsx_strata

Dependencies:abind AnnotationDbi aod askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray DESeq2 farver fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle locfit magrittr Matrix MatrixGenerics matrixStats memoise mime openssl openxlsx pkgconfig plyr png R6 RColorBrewer Rcpp RcppArmadillo RCurl reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys TRESS vctrs viridisLite withr XML XVector yaml zip

magpie Package User's Guide

Rendered frommagpie.Rmdusingknitr::rmarkdown

Last update: 2023-02-19
Started: 2023-01-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
All plots of power evaulation results under various scenarios.	plotAll
All plots of power evaulation results by strata.	plotAll_Strata
An individual Plot of power evaulation results under various scenarios.	plotRes
An individual plot of power evaulation results by strata.	plotStrata
Power calculation results for GSE46705	power.test
Power evaluation for MeRIP-seq data under various study designs.	powerEval
Obtain pre-calculated results from four publicly available MeRIP-seq datasets	quickPower
Write power evaulation results under all scenarios to a .xlsx file.	writeToxlsx
Write power evaulation results of four strata under all sample size scenarios to a .xlsx file.	writeToxlsx_strata