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:
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Fluorescence measurement and normalisation.
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Quantification and control of the yield of the single-cell cDNA amplification taking place in the machine.
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Controls on sequencing yield.
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Quantification of control sequences such as RNA spikes and ribosomal RNA.
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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.
As a system to produce and reproduce formatted reports, we use the
knitr engine.
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