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