Package: distinct 1.17.0
Simone Tiberi
distinct: distinct: a method for differential analyses via hierarchical permutation tests
distinct is a statistical method to perform differential testing between two or more groups of distributions; differential testing is performed via hierarchical non-parametric permutation tests on the cumulative distribution functions (cdfs) of each sample. While most methods for differential expression target differences in the mean abundance between conditions, distinct, by comparing full cdfs, identifies, both, differential patterns involving changes in the mean, as well as more subtle variations that do not involve the mean (e.g., unimodal vs. bi-modal distributions with the same mean). distinct is a general and flexible tool: due to its fully non-parametric nature, which makes no assumptions on how the data was generated, it can be applied to a variety of datasets. It is particularly suitable to perform differential state analyses on single cell data (i.e., differential analyses within sub-populations of cells), such as single cell RNA sequencing (scRNA-seq) and high-dimensional flow or mass cytometry (HDCyto) data. To use distinct one needs data from two or more groups of samples (i.e., experimental conditions), with at least 2 samples (i.e., biological replicates) per group.
Authors:
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distinct.pdf |distinct.html✨
distinct/json (API)
NEWS
| # Install 'distinct' in R: |
| install.packages('distinct', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/simonetiberi/distinct/issues
- Kang_subset - Subset from the 'Kang18_8vs8()' object of the 'muscData' package.
- res - Results from 'distinct_test' function
On BioConductor:distinct-1.17.0(bioc 3.20)distinct-1.16.0(bioc 3.19)
Last updated 2 months agofrom:9bf934128c
Exports:distinct_testlog2_FCplot_cdfsplot_densitiestop_results
Dependencies:abindaskpassbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularCairoclicodetoolscolorspacecpp11crayoncurlDelayedArrayDelayedMatrixStatsdigestdoParalleldoRNGdqrngfansifarverFNNforeachformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttrIRangesirlbaisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigpngR6raggRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressrlangrngtoolsRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscuttleSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsyssystemfontstextshapingtibbleUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| distinct: a method for differential analyses via hierarchical permutation tests | distinct-package distinct |
| Test for differential state between two groups of samples, based on scRNA-seq data. | distinct_test |
| Subset from the `Kang18_8vs8()` object of the 'muscData' package. | Kang_subset |
| Compute FCs and log2-FCs. | log2_FC |
| Plot sample-specific CDFs. | plot_cdfs |
| Plot sample-specific densities. | plot_densities |
| Results from 'distinct_test' function | res |
| Filter significant results. | top_results |