Introduction | Preliminaries | Preparing your own data | Examine the mean-correlation relationship | Using SpQN to remove mean-correlation relationship | Assess the impact of normalization | SessionInfo | References
Package: spqn 1.25.0
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_1.25.0.tar.gz
spqn_1.25.0.zip(r-4.7)spqn_1.25.0.zip(r-4.6)spqn_1.25.0.zip(r-4.5)
spqn_1.25.0.tgz(r-4.6-any)spqn_1.25.0.tgz(r-4.5-any)
spqn_1.25.0.tar.gz(r-4.7-any)spqn_1.25.0.tar.gz(r-4.6-any)
spqn_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
spqn/json (API)
| # 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-1.25.0(bioc 3.24)spqn-1.24.0(bioc 3.23)
networkinferencegraphandnetworknormalization
Last updated from:fb7533c485. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 195 | ||
| linux-devel-x86_64 | NOTE | 332 | ||
| source / vignettes | OK | 270 | ||
| linux-release-x86_64 | NOTE | 338 | ||
| macos-release-arm64 | NOTE | 183 | ||
| macos-oldrel-arm64 | NOTE | 170 | ||
| windows-devel | NOTE | 255 | ||
| windows-release | NOTE | 238 | ||
| windows-oldrel | NOTE | 241 | ||
| wasm-release | OK | 131 |
Exports:get_IQR_condition_expnormalize_correlationplot_IQR_condition_expplot_signal_condition_expqqplot_condition_exp
Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArrayfarvergenericsGenomicRangesggplot2ggridgesgluegtableIRangesisobandlabelinglatticelifecycleMatrixMatrixGenericsmatrixStatsR6RColorBrewerrlangS4ArraysS4VectorsS7scalesSeqinfoSparseArraySummarizedExperimentvctrsviridisLitewithrXVector
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 |