thegranderlab/acidadaptedrnaseq repository overview

⁠acidAdaptedRNAseq

⁠Installation

1. Open R and install the R devtools package (if it is not already installed) with install.packages('devtools').
2. Download and install the acidAdaptedRNAseq package by entering install_github('GranderLab/acidAdaptedRNAseq').
3. Load the package with library(acidAdaptedRNAseq.

⁠Usage

There is only one function included in the package; plotFigure which can be called with either the "go_analysis"or "RNAseq" arguments. This function first replicates the operating system in which the analysis was performed (and thus can take some time to run) after which it renders the analysis file (.Rmd) and opens the resulting analysis in your web browser window. Here you can see the code and functions which have been used for each analysis and the resulting figures reproduced in real-time.

⁠Comments, Bugs, Suggestions

We are more than happy to help you with any questions you might have or hear your suggestions. Please submit these via the repositories issues section.

⁠Advanced usage

For the vast majority of users we imagine that the included plotFigurefunction will be sufficient, although, all hand written functions used for analysis are included in the package. Any functions not included in external package dependencies are included in the R directory with the exception of some of the RNAseq analysis functions which are located in the inst/data-raw directory.