the arkasBasespace library parses the single node json, handling multi-custom fasta upload appresults, multi control appResults, and multi comparisons appResults.
Contains the annotation libraries for Homo-sapiens and Mus-musculus ENSEMBL build 84 and ERCC libraries.
Annotation software for obtaining annotation libraries.
Quantification software which encapsulates and processes Kallisto h5 data.
these are the scripts which process user input JSON files collected during the web-cloud application input selections for Arkas-Quantification/Analysis cloud apps found on Illmina's basespace platform.
arkasBasespace in the analysis function will contain more scripts not related to quantifying on the cloud , but analyzing on the cloud, this arkasBasespace R package is a superset, and should be the final R package for cloud computing.
These are the markdown files which run the analysis pipelines to generate the HTML output file and subsequent analysis files.
Similar to outputReport files, but called from the command line using /bin
If you need to revise parts of the package, edit the libraries in this directory and rebuild arcolombo/arkasanalysisbasespace:v6. this builds ontop of githublayers. so you don't need to re-install R packages or enviroment package dependencies. only need to edit and re-install the last layer specific to arkas.
add steps on maintaining here. (devel use only)
These packages are Licensed by MIT license Copyright 2017 COPYWRIGHT Arkas, Anthony Colombo
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