NEWS.md

In bakR: Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets

bakR 1.0.1

• Updated Stan array syntax to be compatible with current rstan version
• Hack to address Hmisc binning edge case (see https://github.com/harrelfe/Hmisc/issues/169).

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

bakR 0.4.4

• Small edit to configuration files that address compilation issues that can arise on some systems. Deals with "file too big" errors" during package installation from source.

bakR 0.4.3

• Implemented long read sequencing data analysis strategy. Run bakRFit() with Long = TRUE to use k-means clustering (k = 2) for mutation rate and fraction new estimation. Need to have Ckmeans.1d.dp package installed to do this (not installed during bakR installation).

bakR 0.4.2

• Fixed bug in reliableFeatures. high_p was supposed to be the maximum allowable mutation rate (# of mutations/# of Ts) in reads from -s4U controls, but was instead the maximum allowable average number of T-to-C mutations in reads from these controls.

bakR 0.4.1

• Fixed bug in cBprocess that didn't properly check that features of interest provided by the FOI argument were valid.

bakR 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().

bakR 0.3.0

• Optimized data preprocessing with data.table
• Increased simulation flexibility
• Added edge case error catching

bakR 0.2.5

• Added checks to bakRData validator
• Fixed bug in NSSHeatmap that prevented adjusting padj cutoff

bakR 0.2.4

• Addressed NOTEs to prepare for CRAN submission
• Removed previously deprecated function sim_bakRData()

bakR 0.2.3

• Expanded discussion of NSS analysis in vignette

bakR 0.2.2

• Fixed non-steady-state (NSS) uncertainty quantification
• Fixed uncertainty quantification for pulse-chase analysis
• Fixed fraction new estimation for pulse-chase analysis

bakR 0.2.1

• Added pulse-chase analysis option

bakR 0.2.0

• Improved default mutation rate estimation strategy
• Updated vignettes and added back non-steady state analysis strategy discussion
• Better commenting of fast_analysis (instead of opting for refactorization)

bakR 0.1.1

• Changed ordering of vignettes on website
• Got rid of unnecessary stan models and functions
• Fixed TL_stan output documentation
• Corrected missing namespace issues

bakR 0.1.0

• Made bakR public

bakR documentation built on June 22, 2024, 6:55 p.m.