M3Drop: Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Version 1.2.0

This package fits a Michaelis-Menten model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells.

AuthorTallulah Andrews <tallulandrews@gmail.com>
Bioconductor views DifferentialExpression DimensionReduction FeatureExtraction GeneExpression RNASeq Sequencing Software Transcriptomics
Date of publicationNone
MaintainerTallulah Andrews <tallulandrews@gmail.com>
LicenseGPL (>=2)
Version1.2.0
URL https://github.com/tallulandrews/M3Drop
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("M3Drop")

Popular man pages

Brennecke_getVariableGenes: Identify Highly Variable Genes
Fitting_Dropout_Models: Fit functions to the dropouts vs expression distribution.
M3D_Differential_Expression: Differentially Expressed Genes.
M3D_Dropout_Models: Fit functions to the dropouts vs expression distribution.
M3D_Expression_Heatmap: Plot Heatmap of Gene Expression
M3D_getmarkers: Identify marker genes
M3D_ThreeSet_Venn: Three-way Venn Diagram
See all...

All man pages Function index File listing

Man pages

Brennecke_getVariableGenes: Identify Highly Variable Genes
Fitting_Dropout_Models: Fit functions to the dropouts vs expression distribution.
M3D_Clean_Data: Filter Expression Data
M3D_Differential_Expression: Differentially Expressed Genes.
M3D_Dropout_Models: Fit functions to the dropouts vs expression distribution.
M3D_Expression_Heatmap: Plot Heatmap of Gene Expression
M3D_Get_Extremes: Get outliers from MM curve.
M3D_Get_Heatmap_Cell_Clusters: Extracts cell clusters from heatmap output
M3D_getmarkers: Identify marker genes
M3D_Test_Shift: Test for horizontal shift.
M3D_ThreeSet_Venn: Three-way Venn Diagram

Functions

BrenneckeGetVariableGenes Man page Source code
ConvertSetstoTable Source code
M3DropCleanData Man page Source code
M3DropDifferentialExpression Man page Source code
M3DropDropoutModels Man page Source code
M3DropExpressionHeatmap Man page Source code
M3DropGetExtremes Man page Source code
M3DropGetHeatmapCellClusters Man page Source code
M3DropGetMarkers Man page Source code
M3DropTestShift Man page Source code
M3DropThreeSetVenn Man page Source code
PlaceLabels Source code
bg__add_model_to_plot Source code
bg__calc_variables Source code
bg__dropout_plot_base Source code
bg__expression_heatmap Source code
bg__filter_cells Source code
bg__fit_MM Man page Source code
bg__fit_ZIFA Man page Source code
bg__fit_logistic Man page Source code
bg__get_extreme_residuals Source code
bg__highlight_genes Source code
bg__horizontal_residuals_MM_log10 Source code
bg__test_DE_K_equiv Source code
circle_intersection Source code
circle_line_intersection Source code
hidden__UQ Source code
hidden__fit_MM_logistic Source code
hidden__fit_MM_lognormal Source code
hidden__invert_MM Source code
hidden__normalize Source code
hidden__test_DE_K_equiv_raw Source code
hidden__test_DE_P_equiv Source code
hidden__test_DE_S_equiv Source code
hidden_getAUC Source code
plot.venn.diagram Source code
venn.overlap Source code

Files

DESCRIPTION
NAMESPACE
R
R/Brennecke_implementation.R
R/Curve_fitting.R
R/Extremes.R
R/Normalization.R
R/Plotting_fxns.R
R/Threeway_ProportionalArea_VennDiagrams.R
R/basics.R
README
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/M3Drop_Vignette.R
inst/doc/M3Drop_Vignette.Rnw
inst/doc/M3Drop_Vignette.pdf
man
man/Brennecke_getVariableGenes.Rd
man/Fitting_Dropout_Models.Rd
man/M3D_Clean_Data.Rd
man/M3D_Differential_Expression.Rd
man/M3D_Dropout_Models.Rd
man/M3D_Expression_Heatmap.Rd
man/M3D_Get_Extremes.Rd
man/M3D_Get_Heatmap_Cell_Clusters.Rd
man/M3D_Test_Shift.Rd
man/M3D_ThreeSet_Venn.Rd
man/M3D_getmarkers.Rd
vignettes
vignettes/M3Drop_Vignette.Rnw
M3Drop documentation built on May 20, 2017, 9:52 p.m.

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