Package: MEB 1.19.0
Jiadi Zhu
MEB: A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq and scRNA-seq data
This package provides a method to identify differential expression genes in the same or different species. Given that non-DE genes have some similarities in features, a scaling-free minimum enclosing ball (SFMEB) model is built to cover those non-DE genes in feature space, then those DE genes, which are enormously different from non-DE genes, being regarded as outliers and rejected outside the ball. The method on this package is described in the article 'A minimum enclosing ball method to detect differential expression genes for RNA-seq data'. The SFMEB method is extended to the scMEB method that considering two or more potential types of cells or unknown labels scRNA-seq dataset DEGs identification.
Authors:
MEB_1.19.0.tar.gz
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MEB.pdf |MEB.html✨
MEB/json (API)
NEWS
| # Install 'MEB' in R: |
| install.packages('MEB', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- real_data_dsp - A real dataset of genes between the different species.
- real_data_sp - A real dataset of genes between the same species.
- sim_data_dsp - A simulation dataset of genes between the differetn species.
- sim_data_sp - A simulation dataset of genes between the same species.
- sim_scRNA_data - A simulation scRNA-seq dataset from splatter package.
- stable_gene - The name of the stable genes in all dataset.
On BioConductor:MEB-1.19.0(bioc 3.20)MEB-1.18.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:9e57f37581
Dependencies:abindaskpassbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularCairoclassclicodetoolscolorspacecpp11crayoncurlDelayedArrayDelayedMatrixStatsdqrnge1071edgeRfansifarverFNNformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttrIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitloggingmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigpngproxyR6raggRColorBrewerRcppRcppAnnoyRcppEigenRcppHNSWRcppMLRcppProgressrlangRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscuttleSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsyssystemfontstextshapingtibbleUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrwrswoRXVectorzlibbioc
