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SexSeek

SexSeek estimates genetic sex from bulk or single-cell expression counts, using sex-chromosome marker expression and X-inactivation markers. Each sample, donor or cell is called male, female, uncertain, possible_mixed or unknown, with confidence metrics.

Install

install.packages("SexSeek")

# development version
remotes::install_github("saketlab/SexSeek")

Use

library(SexSeek)

path <- system.file("extdata", "example_counts.tsv.gz", package = "SexSeek")
counts <- as.matrix(read.delim(path, row.names = 1))
EstimateSex(counts, group = colnames(counts))

EstimateSex(counts)                          # matrix, sparse matrix, data frame
EstimateSex("counts.tsv.gz")                 # delimited file
EstimateSex("filtered_feature_bc_matrix/")   # 10x MatrixMarket directory
EstimateSex("sample.h5")                     # 10x HDF5
EstimateSex(seurat_obj, group = "donor")     # aggregate by a metadata column

Species is detected from the gene identifiers; pass species = "mouse" (common or scientific name) to set it.

Genevintage annotations

You can provide your own set of sex genes or fetch it from genevintage:

install.packages("genevintage")
sex_genes <- SexChromosomeGenes("human", release = 116, source = "ensembl")
EstimateSex(counts, species = "human", annotation = sex_genes)
EstimateSex(counts, species = "human", annotation = "genevintage")

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.