Single-cell transcriptome analysis by fluorescence labeling
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DDBJ
HiSeq
Intensity_correction
cDNA_concentration
combine_all
control-sequences
fluorescence
AUTHORS.md
LICENSE
README.md
knitr.mk

README.md

Cell-Cycle-on-C1

Single-cell transcriptome analysis by fluorescence labeling.

See our preprint on bioRxiv.

This repository contains source code and explanations on how to control quality in transcriptome analysis of fluorescent cells in the Fluidigm C1 platform. These explanations cover in particular:

As supporting data for these scripts, we provide a RNA-seq analysis of Fucci cells, available in public repositories. Deeper analysis of these data is ongoing and will be the topic of a separate publication.

The authors of the source code in this repository dedicate it to the public domain under the Creative Commons Zero License.

Required software

As a system to produce and reproduce formatted reports, we use the knitr engine.

R libraries:

gdata, ggplot2, knitr, reshape, XML, moments, lattice, flexmix, limma, MASS, rms, contrast

In Debian, some of these libraries are provided by the packages r-cran-gdata, r-cran-ggplot2, r-cran-reshape

Other software:

lftp, Fiji ImageJ