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

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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.

Author
Tallulah Andrews <tallulandrews@gmail.com>
Date of publication
None
Maintainer
Tallulah Andrews <tallulandrews@gmail.com>
License
GPL (>=2)
Version
1.0.0
URLs

View on Bioconductor

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

Files in this package

M3Drop/DESCRIPTION
M3Drop/NAMESPACE
M3Drop/R
M3Drop/R/Brennecke_implementation.R
M3Drop/R/Curve_fitting.R
M3Drop/R/Extremes.R
M3Drop/R/Normalization.R
M3Drop/R/Plotting_fxns.R
M3Drop/R/Threeway_ProportionalArea_VennDiagrams.R
M3Drop/R/basics.R
M3Drop/README
M3Drop/build
M3Drop/build/vignette.rds
M3Drop/inst
M3Drop/inst/NEWS
M3Drop/inst/doc
M3Drop/inst/doc/M3Drop_Vignette.R
M3Drop/inst/doc/M3Drop_Vignette.Rnw
M3Drop/inst/doc/M3Drop_Vignette.pdf
M3Drop/man
M3Drop/man/Brennecke_getVariableGenes.Rd
M3Drop/man/Fitting_Dropout_Models.Rd
M3Drop/man/M3D_Clean_Data.Rd
M3Drop/man/M3D_Differential_Expression.Rd
M3Drop/man/M3D_Dropout_Models.Rd
M3Drop/man/M3D_Expression_Heatmap.Rd
M3Drop/man/M3D_Get_Extremes.Rd
M3Drop/man/M3D_Get_Heatmap_Cell_Clusters.Rd
M3Drop/man/M3D_Test_Shift.Rd
M3Drop/man/M3D_ThreeSet_Venn.Rd
M3Drop/man/M3D_getmarkers.Rd
M3Drop/vignettes
M3Drop/vignettes/M3Drop_Vignette.Rnw