Package: spqn 1.17.0
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:
spqn_1.17.0.tar.gz
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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-1.17.0(bioc 3.20)spqn-1.16.0(bioc 3.19)
Last updated 2 months agofrom:6e3843d381
Exports:get_IQR_condition_expnormalize_correlationplot_IQR_condition_expplot_signal_condition_expqqplot_condition_exp
Dependencies:abindaskpassBiobaseBiocGenericsclicolorspacecrayoncurlDelayedArrayfansifarverGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggridgesgluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerrlangS4ArraysS4VectorsscalesSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
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 |