Introduction | Installation | Example | Data Input | Divergence Matrix Calculation | More on the density method: | More on the divergence method | Visualization | Testing and Confidence intervals | Parallelization and Random Seeds | Random seed | References | SessionInfo
Package: GloScope 2.3.0
Elizabeth Purdom
GloScope: Population-level Representation on scRNA-Seq data
This package aims at representing and summarizing the entire single-cell profile of a sample. It allows researchers to perform important bioinformatic analyses at the sample-level such as visualization and quality control. The main functions Estimate sample distribution and calculate statistical divergence among samples, and visualize the distance matrix through MDS plots.
Authors:
GloScope_2.3.0.tar.gz
GloScope_2.3.0.zip(r-4.7)GloScope_2.3.0.zip(r-4.6)GloScope_2.3.0.zip(r-4.5)
GloScope_2.3.0.tgz(r-4.6-any)GloScope_2.3.0.tgz(r-4.5-any)
GloScope_2.3.0.tar.gz(r-4.7-any)GloScope_2.3.0.tar.gz(r-4.6-any)
GloScope_2.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GloScope/json (API)
| # Install 'GloScope' in R: |
| install.packages('GloScope', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/epurdom/gloscope/issues
Datasets:
- example_SCE - SingleCellExperiment containing example inputs to GloScope
- example_SCE_small - SingleCellExperiment containing example inputs to GloScope
On BioConductor:GloScope-2.3.0(bioc 3.24)GloScope-2.2.0(bioc 3.23)
datarepresentationqualitycontrolrnaseqsequencingsoftwaresinglecell
Last updated from:15d93b858c. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 197 | ||
| linux-devel-x86_64 | OK | 701 | ||
| source / vignettes | OK | 304 | ||
| linux-release-x86_64 | OK | 673 | ||
| macos-release-arm64 | OK | 337 | ||
| macos-oldrel-arm64 | OK | 331 | ||
| windows-devel | OK | 771 | ||
| windows-release | OK | 754 | ||
| windows-oldrel | OK | 773 | ||
| wasm-release | OK | 173 |
Exports:bootCIbootGloscopegetMetricsgloscopegloscopePropplotCIplotHeatmapplotMDS
Dependencies:abindBHBiobaseBiocGenericsBiocParallelbootcliclustercodetoolscpp11DelayedArrayfarverFNNformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglambda.rlatticelifecycleMASSMatrixMatrixGenericsmatrixStatsmclustmgcvmvnfastnlmepermutepheatmapR6RANNRColorBrewerRcppRcppArmadillorlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraySummarizedExperimentvctrsveganviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| SingleCellExperiment containing example inputs to GloScope | example_SCE example_SCE_small |
| Calculate metrics on separation in distance matrix due to grouping variable | bootCI bootGloscope getMetrics |
| Calculate statistical divergence between all sample pairs | gloscope |
| Calculate divergence between all sample pairs' cell type proportion | gloscopeProp |
| Plot confidence intervals | plotCI |
| Plot a heatmap of the GloScope represenation | plotHeatmap |
| Plot the multidimensional scaling of the GloScope represenation | plotMDS |
