Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically increased. Navigating the vast sea of tools now available is becoming increasingly challenging for researchers. In order to better facilitate selection of appropriate analysis tools we have created the scRNA-tools database (www.scRNA-tools.org) to catalogue and curate analysis tools as they become available. Our database collects a range of information on each scRNA-seq analysis tool and categorises them according to the analysis tasks they perform. Exploration of this database gives insights into the areas of rapid development of analysis methods for scRNA-seq data. We see that many tools perform tasks specific to scRNA-seq analysis, particularly clustering and ordering of cells. We also find that the scRNA-seq community embraces an open-source and open-science approach, with most tools available under open-source licenses and preprints being extensively used as a means to describe methods. The scRNA-tools database provides a valuable resource for researchers embarking on scRNA-seq analysis and records the growth of the field over time.
Citation
@article{zappia2018,
author = {Zappia, Luke and Phipson, Belinda and Oshlack, Alicia},
title = {Exploring the Single-Cell {RNA-seq} Analysis Landscape with
the {scRNA-tools} Database},
journal = {PLoS computational biology},
volume = {14},
number = {6},
pages = {e1006245},
date = {2018-06-01},
url = {https://lazappi.id.au/publications/2018-zappia-scRNAtools},
doi = {10.1371/journal.pcbi.1006245},
issn = {1553-734X, 1553-7358},
langid = {en},
abstract = {As single-cell RNA-sequencing (scRNA-seq) datasets have
become more widespread the number of tools designed to analyse these
data has dramatically increased. Navigating the vast sea of tools
now available is becoming increasingly challenging for researchers.
In order to better facilitate selection of appropriate analysis
tools we have created the scRNA-tools database (www.scRNA-tools.org)
to catalogue and curate analysis tools as they become available. Our
database collects a range of information on each scRNA-seq analysis
tool and categorises them according to the analysis tasks they
perform. Exploration of this database gives insights into the areas
of rapid development of analysis methods for scRNA-seq data. We see
that many tools perform tasks specific to scRNA-seq analysis,
particularly clustering and ordering of cells. We also find that the
scRNA-seq community embraces an open-source and open-science
approach, with most tools available under open-source licenses and
preprints being extensively used as a means to describe methods. The
scRNA-tools database provides a valuable resource for researchers
embarking on scRNA-seq analysis and records the growth of the field
over time.}
}