Millefy

Millefy is a tool for visualizing read coverage of single-cell RNA sequensing (scRNA-seq) datasets in genomic contexts. By dynamically and automatically reorder single cells based on 'locus-specific' pseudotime, Millefy highlights cell-to-cell heterogeneity in read covreage of scRNA-seq data.

Millefy is available as an R package and a Docker image with JupyterLab.

Example of millefy plot

Getting started

Installation

install.packages(c("data.table", "dtplyr", "proxy", "viridisLite"), dependencies=TRUE)


# For R < 3.5.0 users
source("https://bioconductor.org/biocLite.R"); biocLite()
biocLite(c('Rsamtools', 'GenomicRanges',  'rtracklayer', 'destiny'))

# For R >= 3.5.0 users
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c('Rsamtools', 'GenomicRanges',  'rtracklayer', 'destiny'))


devtools::install_github("yuifu/millefy")

Requirements

• R (version 3.2.2 or higher)

Quick example

To quickly learn to use Millefy, try out Quick example with the included example dataset.

Learning more

See Tutorial for details.