Package: Anaquin 2.31.0

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

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Anaquin.pdf |Anaquin.html✨
Anaquin/json (API)
NEWS

# 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-2.31.0(bioc 3.21)Anaquin-2.30.0(bioc 3.20)

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

4.65 score 45 scripts 278 downloads 5 exports 83 dependencies

Last updated 2 months agofrom:6b70356720. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:plotConjoint plotLinear plotLOD plotLogistic plotROC

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel bitops caTools cli codetools colorspace cpp11 crayon curl DelayedArray DESeq2 evaluate fansi farver formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gplots gtable gtools highr httr IRanges isoband jsonlite KernSmooth knitr labeling lambda.r lattice lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig plyr qvalue R6 RColorBrewer Rcpp RcppArmadillo reshape2 rlang ROCR S4Arrays S4Vectors scales snow SparseArray stringi stringr SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc

Anaquin - Vignette

Ted Wong ([email protected])

Rendered fromAnaquin.Rmdusingknitr::rmarkdownon Nov 29 2024.

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