Package: Anaquin 2.37.0

Ted Wong

Anaquin: Statistical analysis of sequins

The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls.

Authors:Ted Wong

Anaquin_2.37.0.tar.gz
Anaquin_2.37.0.zip(r-4.7)Anaquin_2.37.0.zip(r-4.6)Anaquin_2.37.0.zip(r-4.5)
Anaquin_2.37.0.tgz(r-4.6-any)Anaquin_2.37.0.tgz(r-4.5-any)
Anaquin_2.37.0.tar.gz(r-4.7-any)Anaquin_2.37.0.tar.gz(r-4.6-any)
Anaquin_2.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Anaquin/json (API)

# Install 'Anaquin' in R:

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

Datasets:

RnaQuinGeneMixture - RnaQuin mixture
RnaQuinIsoformMixture - RnaQuin mixture
UserGuideData_5.4.5.1 - Section 5.4.5.1 Assembly Dataset
UserGuideData_5.4.6.3 - Gene expression
UserGuideData_5.6.3 - Differential expression

On BioConductor:Anaquin-2.37.0(bioc 3.24)Anaquin-2.36.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology differentialexpression preprocessing rnaseq geneexpression software

4.69 score 49 scripts 5 exports 63 dependencies

Last updated from:aa820db8f9. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	159
linux-devel-x86_64	NOTE	199
source / vignettes	OK	197
linux-release-x86_64	NOTE	207
macos-release-arm64	NOTE	114
macos-oldrel-arm64	NOTE	104
windows-devel	NOTE	126
windows-release	NOTE	116
windows-oldrel	NOTE	124
wasm-release	OK	164

Exports:plotConjoint plotLinear plotLOD plotLogistic plotROC

Dependencies:abind BH Biobase BiocGenerics BiocParallel bitops caTools cli codetools cpp11 DelayedArray DESeq2 evaluate farver formatR futile.logger futile.options generics GenomicRanges ggplot2 glue gplots gtable gtools highr IRanges isoband KernSmooth knitr labeling lambda.r lattice lifecycle locfit magrittr Matrix MatrixGenerics matrixStats plyr qvalue R6 RColorBrewer Rcpp RcppArmadillo reshape2 rlang ROCR S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment vctrs viridisLite withr xfun XVector yaml

Anaquin - Vignette

Rendered fromAnaquin.Rmdusingknitr::rmarkdown

Last update: 2017-08-08
Started: 2016-08-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create conjoint plots	plotConjoint
Plot linear model for sequins	plotLinear
Create Limit-of-Detection Ratio (LOD) plot	plotLOD
Plot logistic model for sequins	plotLogistic
Create ROC plot	plotROC
RnaQuin mixture (gene level)	RnaQuinGeneMixture
RnaQuin mixture (isoform level)	RnaQuinIsoformMixture
Section 5.4.5.1 Assembly Dataset	UserGuideData_5.4.5.1
Gene expression (RnaQuin)	UserGuideData_5.4.6.3
Differential expression (RnaQuin)	UserGuideData_5.6.3