index.md

In jmw86069/farrisdata: Farris et al Mouse Hippocampus RNA-seq data objects

farrisdata

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:

• https://github.com/jmw86069/jampack

This package includes a data.frame for use by splicejam::prepareSashimi() to create Sashimi coverage plots of transcriptome RNA-seq data, see:

• https://github.com/jmw86069/splicejam

How to install

Install using the R package devtools and this command:

devtools::install_github("jmw86069/farrisdata")

To install splicejam and/or jampack:

devtools::install_github("jmw86069/splicejam")
devtools::install_github("jmw86069/jampack")

Literature references:

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

jmw86069/farrisdata documentation built on Oct. 8, 2019, 9:56 p.m.