Package: spqn 1.19.0

Yi Wang

spqn: Spatial quantile normalization

The spqn package implements spatial quantile normalization (SpQN). This method was developed to remove a mean-correlation relationship in correlation matrices built from gene expression data. It can serve as pre-processing step prior to a co-expression analysis.

Authors:Yi Wang [cre, aut], Kasper Daniel Hansen [aut]

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

# Install 'spqn' in R:

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

Bug tracker:https://github.com/hansenlab/spqn/issues

On BioConductor:spqn-1.19.0(bioc 3.21)spqn-1.18.0(bioc 3.20)

networkinference graphandnetwork normalization

5.04 score 5 stars 22 scripts 134 downloads 5 exports 55 dependencies

Last updated 23 days agofrom:ebac31513d. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

Exports:get_IQR_condition_exp normalize_correlation plot_IQR_condition_exp plot_signal_condition_exp qqplot_condition_exp

Dependencies:abind askpass Biobase BiocGenerics cli colorspace crayon curl DelayedArray fansi farver generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggridges glue gtable httr IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig R6 RColorBrewer rlang S4Arrays S4Vectors scales SparseArray SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Spatial quantile normalization for co-expression analysis

Yi Wang, Kasper D. Hansen

Rendered fromspqn.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-04-13
Started: 2019-10-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Spatial quantile normalization	spqn-package spqn
Spatial quantile normalization (SpQN)	normalize_correlation
Get and plot the IQRs of submatrices of the correlation matrix.	get_IQR_condition_exp plot_IQR_condition_exp
Plot the signal and background distribution of a correlation matrix.	plot_signal_condition_exp
Q-Q plot for examing the distributions across submatrices of a correlation matrix.	qqplot_condition_exp