This R package is created and maintained by Nikos Karaiskos.
It offers a quick and straightfoward way to explore and perform
basic analysis of single cell sequencing data coming from droplet
sequencing. It has been particularly tailored for Drop-seq.
Dropbead accompanies the following publication and was used to generate all figures appearing in the manuscript prior clustering.
Cell fixation and preservation for droplet-based single-cell transcriptomics,
BMC Biology 2017 15:44,
bioRxiv, 99473 (2017)
doi: https://doi.org/10.1101/099473
J. Alles#, N. Karaiskos#, S. Praktiknjo#, S. Grosswendt, P. Wahle, P.-L. Ruffault, S. Ayoub, L. Schreyer, A. Boltengagen, C. Birchmeier, R. Zinzen, C. Kocks& and N. Rajewsky&
# Contributed equally
& Corresponding authors: C. Kocks, N. Rajewsky
Contact the author in case you've found a bug. Feel free to cite the package in case you've used it.
The easiest way to install dropbead is through devtools
library(devtools)
install_github("rajewsky-lab/dropbead")
A first walkthrough is found in the tutorial. As the file's size is currently
too big for Github, to view the tutorial click on the .html file, then on the
raw format and save it locally. You can then view the tutorial with an
ordinary web browser.