MSC dissertation and supporting material

The dissertation document can be found in a pdf format and is called "nsc_msc_diss"

Included in this repo is the version of CircadianTools, an R package developed for the dissertation, used for analysis in the dissertation. This package can be installed using the instructions included in the CircadianTools appendix found in the main document or by following the instructions in the below section.

For ease of use, an uncompressed folder containing all of the source code for CircadianTools can be found in the R directory.

The R markdown directory contains R markdown files which can be run to reproduce the results presented in the dissertation. Also included in this directory is any saved file which is produced by the R markdown files.

The Raw_Data folder contains the raw T. saltator transcriptomics data which was used for this project which has been acquired from Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltator by O'Grady et al.

CircadianTools Installation

Please note either a MacOS or Linux/GNU system is recommended for CircadianTools due to the use of Forked clusters for parallel calculations.

Installing the CircadianTools R package is best done through the use of the devtools package as this will ensure all of the packages which CircadianTools depends on will also be installed. Running the below code in R will install the devtools package.

install.packages("devtools")

Before CircadianTools can be installed, dependencies from Bioconductor must also be installed. This can be done by using the following R command:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("rain", "seqinr")

The most up-to-date version of CircadianTools can be installed from Github by entering the below line in to the R console:

devtools::install_github("nathansam/CircadianTools")

Included in this repo is the most recent version of the CircadianTools at the time of submission. This version of the package can be installed by the devtools::install_local("path") function where "path" is the path to the included "CircadianTools_1.0.0.tar.gz" file For example, if the "CircadianTools_1.0.0.tar.gz" file is moved to my linux desktop then CircadianTools can be installed by the following command:

devtools::install_local("/home/nathan/desktop/CircadianTools_1.0.0.tar.gz")