We are looking for a bioinformatics postdoctoral fellow.  The successful candidate has a PhD in bioinformatics or computational biology.  Strong interest in single cell trajectory analysis, and creative ability in data presentation, computer animation, and enthusiasm for bioart/biocreativity is a requirement. We expect strong work ethics, vision, and ability to independently learn and implement new technologies.

If you are interested, please send a single introductory paragraph and your CV to Stefan Heller at hellers@stanford.edu

 

CellTrails: Reconstruction, Visualization, and Analysis of Branching Trajectories from Single-cell Expression Data

Software implementation by Daniel Christian Ellwanger

Department of Otolaryngology – Head & Neck Surgery, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA

CellTrails is an unsupervised algorithm for the de novo chronological ordering, visualization and analysis of single-cell expression data. CellTrails makes use of a geometrically motivated concept of lower-dimensional manifold learning, which exhibits a multitude of virtues that counteract intrinsic noise of single cell data caused by drop-outs, technical variance, and redundancy of predictive variables. CellTrails enables the reconstruction of branching trajectories and provides an intuitive graphical representation of expression patterns along all branches simultaneously. It allows the user to define and infer the expression dynamics of individual and multiple pathways towards distinct phenotypes.

CellTrails was developed with a 183-dimensional RT-qPCR gene expression panel of 1,008 cells collected from the developing chicken utricle, a balance organ. Key players in the utricle’s function are cohorts of sensory hair cells that display mechanosensing organelles, called hair bundles, protruding from their apical surfaces. Bundle growth and maturation is dictated by an orchestration of distinct sequential and overlapping cellular processes. Our goal was to elucidate the temporal expression program of key hair bundle genes in subtypes of hair cells that occur with distinct spatial distribution. We showed that CellTrails faithfully predicted expression patterns of hair cell maturation with unprecedented resolution.

We confirmed that CellTrails can be applied to analysis of single-cell RNA-Seq datasets. We are pleased that you consider using CellTrails in your research. A detailed theoretical description of the algorithm and its application to biological uses has been published in:

Ellwanger DC, Scheibinger M, Dumont RA, Barr-Gillespie PG, and Heller S. “Transcriptional dynamics of hair-bundle morphogenesis revealed with CellTrails”. Cell Reports 2018 Jun 5;23(10).

News

Installation

Prerequisites

CellTrails is an extension for R (https://www.r-project.org), which is a free software environment for statistical computing and graphics. Please note that an installation of R is required for using CellTrails.

A simple yet efficient way to work with R consists in writing source code with your favorite text editor and sending it to the R console. It is suggested to use a development environment, such as Rstudio (https://www.rstudio.com/), or a rich text editor with R functionalities, such as Emacs (https://www.gnu.org/software/emacs/), which greatly eases the work.

We also recommend to download and install the graph visualization software yEd (http://www.yworks.com/products/yed). It provides great capabilities to visualize and analyze a trajectory graph produced by CellTrails.

CellTrails

The CellTrails package itself can be installed directly from Bioconductor within an active R session:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("CellTrails", version = "3.8")

 

Alternatively, the most recent developmental version can be obtained from Github using the devtools package within an active R session:


devtools::install_github("dcellwanger/CellTrails", build_vignettes=TRUE)

Load package

After its successfull installation, the package can be loaded within an active R session as follows:


library(CellTrails)

User manual

The CellTrails Handbook is available here.

Frequently Asked Questions

An error message was shown during installation. What should I do?

If the following message is shown:


Error in loadNamespace(name) : there is no package called 'devtools'.

Then your R distrubution is missing the devtools package. Please install the devtools package as follows:


install.packages("devtools")
devtools::install_github("dcellwanger/CellTrails", build_vignettes=TRUE)

 

If the following message is shown:


An error message was shown during installation: Error: package or
namespace load failed for ‘GenomeInfoDb’ in
loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’ Error :
package ‘GenomeInfoDb’ could not be loaded.

Then the package dependencies were not properly resolved automatically. Please, install the missing packages manually as follows:


source("https://bioconductor.org/biocLite.R")
biocLite("GenomeInfoDb", "GenomeInfoDbData")
devtools::install_github("dcellwanger/CellTrails", build_vignettes=TRUE)

 

CellTrails is not sucessfully installed using devtools.
If the installation with devtools is not successfull, you may need to install CellTrails‘ dependencies manually.


install.packages("cba", "dendextend", "dtw", "EnvStats",
                 "ggplot2", "ggrepel", "igraph", "maptree", "mgcv",
                 "reshape2", "Rtsne", "rmarkdown", "knitr", "RUnit")

source("https://bioconductor.org/biocLite.R")
biocLite("BiocGenerics", "SingleCellExperiment", "Biobase",
         "SummarizedExperiment", "AnnotationDbi", "destiny",
         "GenomeInfoDb", "GenomeInfoDbData",
         "scater", "scran", "org.Mm.eg.db")

devtools::install_github("dcellwanger/CellTrails", build_vignettes=TRUE)

However, we strongly advise to install CellTrails from Bioconductor (see Installation).

 

Do I need to install Xquartz?
If you are using macOS X, we recommend to install XQuartz, a version of the X.Org X Window
System (X11) that runs on OS X (http://xquartz.org). Although CellTrails does not require its installation, it is generally needed if you want to make use of X11
(including tcltk) in R. Please note, that it also needs to be re-installed when upgrading your macOS to a new major version (https://cran.r-project.org/bi/macosx/).

Do I get notified about updates?
Not yet. We recommend to check for updates regularly.

How can I update the package?
The package can be updated by installing the most recent version using devtools.

Is the package be available at Bioconductor.org?
Yes, CellTrails has been accepted at Bioconductor (DOI: 10.18129/B9.bioc.CellTrails) and can be obtained at http://bioconductor.org/packages/devel/bioc/html/CellTrails.html.

How is CellTrails licensed?
CellTrails is licensed under Artistic 2.0 and, therefore, free for use.