caravagnalab/devil

devil

devil

devil is a package to perform differential expression analysis for scRNA-seq dataset considering either single- or multi-patients experimental designs

Installation

You can install the development version of devil from GitHub with:

devtools::install_github("caravagnalab/devil")

Example

This is a basic example which shows you how to fit the expression for a single gene observed in 1000 cells.

library(devil)
y <- t(as.matrix(rnbinom(1000, 1, .1)))
fit <- devil::fit_devil(input_matrix=y, design_matrix=matrix(1, ncol = 1, nrow = 1000), verbose=T, size_factors=T, overdispersion = T)
#> Compute size factors
#> Skipping size factor estimation! Only one gene is present!
#> Initialize beta estimate
#> Fit beta coefficients
#> Fit overdispersion
test <- devil::test_de(fit, c(1))

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Copyright and contacts

Giulio Caravagna, Giovanni Santacatterina. Cancer Data Science (CDS) Laboratory.

devil's Issues

matrixStats error in fit_devil

I am trying to run fit_devil function and I got this error:

> fit <- fit_devil(counts, design_matrix, overdispersion = T, size_factors = T, verbose = T, parallel = T)
Compute size factors
Error: [matrixStats (>= 1.2.0)] useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. See also ?matrixStats::matrixStats.options