RamsinghLab/arkas_staging: A package that complements Kallisto for quick, informative *seq analysis

This package wraps various aspects of workflow automation (assembling transcriptomes, hashing indices after they have been built, checking versions, and generally avoiding annoyance factors) useful in the day-to-day operation of a transcriptome pseudoaligner/quantifier. Tools for data extraction and (progressive) annotation of combined or individual transcriptomes, quality control and normalization (ERCC control plots and RUVSeq normalization), interpretation (gene-level, transcript-level, pathway- and network-level output), and interactions with cloud computing services such as BaseSpace are loosely coupled within the default package workflow. Please be aware that, while Arkas is licensed under the GPL, Kallisto itself is free FOR NON-COMMERCIAL USAGE ONLY. For-profit use of Kallisto requires a licensing agreement executed with the Regents of the University of California. Kallisto is not included within this package; Arkas assumes it is in the user's PATH. Arkas' component parts are not restricted in this fashion (although we cannot guarantee that all [pseudo]aligners will necessarily work as well as Kallisto in end-to-end pipelines), and most downstream analyses can proceed from any SummarizedExperiment. Arkas' annotation functions, in particular, can greatly ease data integration, as when comparing in-house results to those of major genome and transcriptome sequencing projects such as TCGA and ICGC.

install.packages("remotes")
remotes::install_github("RamsinghLab/arkas_staging")