R package containing gene and transcript expression data supporting Farris et al Mouse hippocampal transcriptome RNA-seq analysis.
This data is intended for analysis
using the jampack
R package, also available through
GitHub, see:
This package includes a data.frame
for use by
splicejam::prepareSashimi()
to create Sashimi coverage
plots of transcriptome RNA-seq data, see:
Install using the R package devtools
and this command:
devtools::install_github("jmw86069/farrisdata")
A full set of documentation is provided using the pkgdown::build_site()
function, and is available here:
This package contains two reference SummarizedExperiment
objects,
which are described in more detail in the corresponding R help pages.
The package also provides three reference gene lists containing detected genes in hippocampal CA1 in mouse and rat (Nakayama et al. 2017, Ainsley et al., 2014, Cajigas et al. 2012).
Lastly, the package provides a color substitution vector colorSub
,
and several vectors with derived transcript features.
Nakayama, K., Ohashi, R., Shinoda, Y., Yamazaki, M., Abe, M., Fujikawa, A., Shigenobu, S., Futatsugi, A., Noda, M., Mikoshiba, K., Furuichi, T., Sakimura, K., Shiina, N., 2017. RNG105/caprin1, an RNA granule protein for dendritic mRNA localization, is essential for long-term memory formation. eLife 6, e29677. doi:10.7554/eLife.29677
Ainsley, J.A., Drane, L., Jacobs, J., Kittelberger, K.A., Reijmers, L.G., 2014. Functionally diverse dendritic mRNAs rapidly associate with ribosomes following a novel experience. Nature Communications 5, 4510. doi:10.1038/ncomms5510
Cajigas, I.J., Tushev, G., Will, T.J., tom Dieck, S., Fuerst, N., Schuman, E.M., 2012. The local transcriptome in the synaptic neuropil revealed by deep sequencing and high-resolution imag-ing. Neuron 74, 453–466. doi:10.1016/j.neuron.2012.02.036
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