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bakR 1.0.1

bakR 1.0.0

CRAN release: 2023-06-29

  • 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

CRAN release: 2023-03-14

  • 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

CRAN release: 2022-10-10

  • 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