NEWS.md
In calebclass/NanoTube: An Easy Pipeline for NanoString nCounter Data Analysis

processNanostringData now reads RCC files recursively from the parent directory, so that it can handle RCC files within subfolders.

Corrected a bug in positiveQC(), which caused it to calculate different positive scale factors from normalize_pos_control(); the second was confirmed to be correct.

runLimmaAnalysis now allows optional arguments, which are passed to limma::lmFit.

The codeclass.retain option now allows runLimmaAnalysis() to be run using a CodeClass/CodeClasses specified by the user, instead of automatically removing non-endogenous genes. See help(runLimmaAnalysis) for details.
processNanostringData() can now handle a vector of .rcc files, in addition to the previous options for loading NanoString data.

In addition to ruv::RUVIII, the RUVSeq::RUVg method can now be used for data normalization. Options have also been added to allow tuning of the parameters for these methods. More details are provided in the vignette.
A csv or txt file containing a design matrix can be input as a 'sampleTab' in processNanostringData(). This facilitates easier differential expression analysis with more complex models, and an example has been added to the vignette.
Various other improvements to vignette.

NanoTube can now process zipped and tarred (.zip or .tar) directories, as well as gzipped (.gz) RCC files, such as those downloaded from GEO in many cases.

Corrected a bug that caused NanoTube not to recognize reporters labeled as "Endogenous1", "Endogenous2", etc. as Endogenous.

When processing a folder containing RCC files, processNanostringData() now ignores filenames not ending in "RCC" (case-insensitive).
Corrected a bug that in read_cpdb_sourceDBs() and read_cpdb_tab() that sometimes led to the data being misread.