bakR 1.0.1

Version 1.0.1 of bakR, submitted to CRAN. Biggest change is use of new Stan array syntax to prevent breakage with next rstan release.

bakR 1.0.0

• Functions for visualizing (VisualizeDropout), quantifying (QuantifyDropout), and correcting (CorrectDropout) metabolic label-induced dropout of RNA during library preparation have been added.
• New simulation function (simulate_relative_bakRData) which better captures the relative nature of RNA-seq and can accurately simulate dropout.
• New experimental function (DissectMechanism) for determining how likely that any observed differential expression is driven by transcriptional or post-transcriptional regulation. DissectMechanism is a rewrite and extension of the previously developed NSSHeat2 function, which itself was an improvement of the now deprecated NSSHeat.
• Can now provide fraction new estimates (e.g., from a tool like GRAND-SLAM) as input to bakR. GRAND-SLAM input functionality is further supported by the new GSprocess function that will facilitate converting from GRAND-SLAM output to bakR input.
• FnPCA has been deprecated in favor of FnPCA2 which accepts input differently and fixes some bugs.
• Read count filtering now includes two filters. One read count that all samples must pass, and one that only all replicates in a single Exp_ID need to pass. This facilitates identifying large increases or decreaes in expression.
• Several new vignettes to discuss much of the new functionality discussed above.
• Several small bug fixes

CRAN release 0.4.0

• Added QC_check(), a function to perform quality control analysis with bakRFit objects. Looks for any problems in your data that will impair bakR's performance, generates a number of diagnostic visualizations, and makes suggestions about what to do next.
• Fixed plot coloring bug in plotMA() and plotVolcano().
• Fixed bug that led to problems when the number of -s4U replicates > +s4U replicates in one or more Exp_IDs
• Implemented improved U-content adjustment for MCMC implementation. Also impacts accuracy of StanRateEst = TRUE mutation rate estimation strategy.
• Increased default number of features to use for StanRateEst mutation rate estimation strategy.
• Improved scaling of NSSHeat() output matrix columns.
• Created a new function NSSHeat2() that implements a different mechanism scoring function than NSSHeat().

CRAN release 0.2.4

First release of bakR on CRAN.

bakR 0.2.3

This is version 0.2.3 of bakR. It is likely the last release that one can use to exactly reproduce the results to the version of bakR used in our manuscript.