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:

• Fluorescence measurement
  and normalisation.

• Quantification and control of the yield
  of the single-cell cDNA amplification taking place in the machine.

• Controls on sequencing yield.

• Quantification of control sequences
  such as RNA spikes and ribosomal RNA.

• Aggregation and consistency checks of these data.

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