Changes in version 1.19.8
- ExoLabel has a new parameter to tune the performance of hop-length
attenuation.
- Documentation and formatting updates.
Changes in version 1.19.7
- ExoLabel now uses hop-length attenuation to mitigate formation of
massive communities.
- ExoLabel no longer supports inflation, since attentuation does a
better job handling this without introducing additional parameters.
- ExoLabel will now print a lot less when running with verbose=TRUE in
non-interactive mode -- just as informative, but less junk caused by
lots of unrendered carriage returns.
Changes in version 1.19.6
- fixes multiple bugs in EstimRearrScen
Changes in version 1.19.5
- fixes bug in GeneVector.EvoWeaver that could affect DNA-based
analyses
Changes in version 1.19.4
- fixes bug that prevented building on Windows
- adds multiple clustering support for ExoLabel
Changes in version 1.19.3
- ExoLabel will no longer crash when given a network lacking a
trailing newline
- Various internal improvements and code refinements
Changes in version 1.19.2
- Lots of bug fixes for ExoLabel
- ExoLabel now reports disk consumption during execution
Changes in version 1.19.1
- ExoLabel is even faster due to in-place external sort for faster
file I/O
- Other quality of life improvements to ExoLabel
Changes in version 1.19.0
- First development version of Bioconductor 3.21
Changes in version 1.18.0
- Official Bioconductor 3.20 release
Changes in version 1.17.7
- ExoLabel is much much faster and does a better job cleaning up when
aborted early
- ExoLabel now has fewer arguments
- Updates to man pages
Changes in version 1.17.6
- Lots of internal improvements to ExoLabel to increase computational
speed and decrease disk usage.
- ExoLabel will no longer crash if given relative paths.
- Adds more internal error checking to prevent some rare bugs.
- Updates man pages to reflect new changes.
- Updates EstimateExoLabel to reflect new changes.
Changes in version 1.17.5
- ExoLabel will no longer brick R during sorts on large files.
- ExoLabel reports more progress during some lengthy processing
sections when verbose=TRUE
- Known issue: "Copying source file" step is still non-interruptable,
will be fixed in a later update
Changes in version 1.17.4
- ExoLabel now allows an inflation argument to control application of
inflation
Changes in version 1.17.3
- predict.EvoWeaver now supports returning p-values separately from
raw score for some algorithms.
- OpenMP implementation for EvoWeaver algorithms that support it has
been fixed
Changes in version 1.17.2
- RandForest function added to train random forest models
- Associated man pages for RandForest and DecisionTree objects
- New methods for DecisionTree objects to plot and coerce to
dendrogram
- Small bugfix to subset.dendrogram
Changes in version 1.17.1
- Major updates to EvoWeaver:
- predict.EvoWeaver now returns a data.frame by default
- Method arguments are updated to match their names in the
associated EvoWeaver manuscript
- Above changes have propagated to documentation files
- New Phylogenetic Profiling methods with improved accuracy
- New meta-methods PhylogeneticProfiling, PhylogeneticStructure,
GeneOrganization, SequenceLevel for predict.EvoWeaver
- New pre-trained Ensemble models have been included
- Updates to ExoLabel for better status printing
Changes in version 1.16.0
- Bioc 3.19 release
Changes in version 1.15.3
- Addition of FastLabelOOM function to find communities in
graphs/networks on disk space.
Changes in version 1.15.2
- Addition of PrepareSeqs function, beginning the process of
deprecating PairSummaries in favor of more cohesive and user
friendly functions.
Changes in version 1.15.1
- Fixes bug in JRF distance causing scores to be higher than expected.
Changes in version 1.13.8
- Updates to all EvoWeaver documentation files
- Fixed small bug in PhyloDistance causing Method='JRF' to return
similarity rather than the distance
- Fixed small bug in TreeDistance.EvoWeaver resulting in an
inconsistent calculation of score when using TreeMethods='JRF'
Changes in version 1.13.7
- Small fixes
Changes in version 1.13.6
- ProtWeaver and ProtWeb have been renamed to EvoWeaver and EvoWeb,
respectively
- New sequence level method for EvoWeaver
- Various small internal updates to EvoWeaver
Changes in version 1.13.5
- Minor changes to SelectByK and vignette
Changes in version 1.13.4
- New predictor PAPV.ProtWeaver to calculate p-values for
presence/absence profiles.
- ContextTree now uses MirrorTree with species tree correction and p/a
overlap correction
- Updates to documentation
Changes in version 1.13.3
- predict.ProtWeaver now supports multiple algorithms at once (ex.
predict(ew, Method=c("Jaccard", "Hamming")))
- Documentation for ProtWeaver and associated methods has been updated
to match recent updates.
Changes in version 1.13.2
- FastQFromSRR function added as a convenience wrapper for the
SRAtoolkit function fastq-dump.
Changes in version 1.13.1
- SuperTree now works directly with dist objects, providing better
performance and scaling
- Updates to simMat objects
- No longer throw a warning when initialized in RStudio
- Formatting is cleaner and supports larger object names
- Updates to NVDC.ProtWeaver
- Now supports amino acid sequences using the DNAseqs=FALSE
argument
- Now calculates a p-value-weighted score
- Adds MakeBlastDb function to create a BLAST database from R, plus
associated documentation updates
- Smaller fixes to some ProtWeaver methods
- predict.ProtWeaver no longer returns using invisible (this was
annoying and unneccessary)
- APC correction for MutualInformation.ProtWeaver removed to allow
for parallelization
- MirrorTree.ProtWeaver now works correctly with
MTCorrection="speciestree"
- CorrGL.ProtWeaver now uses Fisher's Exact Test for p-values
rather than the R value of spearman correlation
- Many internal performance improvements
- ProtWeaver almost entirely uses dist objects rather than matrix,
saving significantly on memory
- faster Cophenetic function implemented internally
- Copied internal .Call('cophenetic') from DECIPHER to SynExtend
to avoid potential namespace issues
- Small fixes to remove some notes from BiocCheck::BiocCheck()
- Variety of small updates to pass BiocCheck
Changes in version 1.12.0
- Official Bioconductor 3.17 release (even with SynExtend 1.11.8)
Changes in version 1.11.8
- Fixes various small bugs in MoransI
- Adds some multiprocessing support (more will be added in the future)
- Slight rework to species trees and their interaction with ProtWeaver
objects
- ProtWeaver has new attribute speciesTree, can be initialized
with a dendrogram object
- New method SpeciesTree to get species tree from a ProtWeaver
object (or compute one, if it doesn't exist)
- Various internal improvements for Bioc style consistency
- Various documentation updates
Changes in version 1.11.7
- Adds new optimized dendrapply implementation (overloads
stats::dendrapply)
- AddsHungarianAlgorithm for optimal solving of the linear assignment
problem (O(n^3) complexity)
- Adds new C code for fast computation of Pearson's R and p-value
- Adds new Ancestral.ProtWeaver algorithm for calculating coevolution
from correlated residue changes
- Supporting code and documentation for Ancestral.ProtWeaver
- Other new internal methods
- Various updates and optimizations to internal methods and
documentations
- Updates GRF method to be called CI (for Clustering Information
Distance)
- Method="CI" in PhyloDistance now calculates an approximate p-value
using simulated data from Smith (2020)
Changes in version 1.11.6
- Adds new Residue method NVDT using gene sequence Natural Vector with
Dinucleotide and Trinucleotide frequency
- Adds some new C methods to speed up calculation of NVDT
- Fixes .Call() not using PACKAGE="SynExtend"
- Updates to documentation
Changes in version 1.11.5
- Adds new colocalization algorithm ColocMoran, uses Coloc with
MoransI to correct for phylogenetic signal
- Adds new colocalization algorithm TranscripMI, uses mutual
information of transcriptional direction
- Adds new corrections/checks to allow for transcriptional direction
to be in labels
- Various bugfixes to support new four number labelling scheme
- Various documentation updates
- Adds new function MoransI to calculate Moran's I for a set of
spatially distributed signals
Changes in version 1.11.4
- Internal code refactor
- ShuffleC now supports reproducibility using R's set.seed
- ShuffleC now support sampling with replacement, performance is
around 2.25x faster than sample
Changes in version 1.11.3
- Internal bugfixes for JRF Distance--previous commit was incorrectly
calculating values
- Adds new TreeDistance predictor for ProtWeaver, incorporating all
tree distance metrics; these metrics are bundled due to some backend
optimizations that improve performance
- Bugfixes for PhyloDistance
- Adds Random Projection for MirrorTree predictor to solve memory
problems and increase accuracy
- New internal random number generator using xorshift, significantly
faster than sample()
- HammingGL changed to CorrGL, now uses Pearson's R weighted by
p-value
- Refactors internal predictors to reduce size of codebase and remove
redundancies
- Internal ShuffleC function to replicate sample functionality
with 2-6x speedup
- Method GainLoss now uses bootstrapping to estimate a p-value
- Updates to documentation files
Changes in version 1.11.2
- Adds KF Distance for trees
- Adds Jaccard Robinson Foulds Distance for trees
- Reworks tree distances into PhyloDistance function
- Numerous new documentation pages
- Updates internal functions to use rapply instead of dendrapply to
avoid stack overflow issues due to R recursion
Changes in version 1.11.1
- Minor bugfix to RF distance
- updates gitignore for workflows
Changes in version 1.10.1
- Memory leak bugfix
Changes in version 1.9.21
- Adds new RFDist function to calculate Robinson-Foulds Distance
- Adds normalization for GeneralizedRF to make the distance between 0
and 1
- Minor bugfixes
- Documentation for new functions
Changes in version 1.9.20
- Adds new GeneralizedRF function to calculated information-theoretic
Generalized Robinson-Foulds distance between two dendrograms.
- Documentation for new function
- New ProtWeaver predictor based off of GeneralizedRF metric
- New internal C source code for GeneralizedRF
Changes in version 1.9.19
- Adds new DPhyloStatistic function to calculate the D-statistic for a
binary state against a phylogeny following Fritz and Purvis (2009).
- Documentation for new function
- new internal C source code for DPhyloStatistic
- new internal C source code for random utility functions, currently
only has functions to generate random numbers
Changes in version 1.9.18
- Various internal improvements to presence/absence profile methods
Changes in version 1.9.17
- Adds new prediction algorithm GainLoss
- Adds new internal C implementation of dendrograms, significantly
faster than R dendrograms
- ProtWeaver methods Behdenna and GainLoss can now infer a species
tree when possible
- Updates Jaccard and Hamming methods to use C implementations for
distance calculation
- Adds HammingGL method to calculate Hamming distance of gain/loss
events
- Minor bugfixes to ProtWeaver methods relating to subsetting
- Updates to various man pages
Changes in version 1.9.16
- Removes flatdendrapply, function was already included in SynExtend
- minor bugfixes to ProtWeaver
Changes in version 1.9.15
- Edits to SelectByK, function can work as intended, but is still too
conservative at false positive removal.
Changes in version 1.9.14
- Adds new function flatdendrapply for more options to apply functions
to dendrograms. Function is used in SuperTree.
- Adds new function SuperTree to construct a species tree from a set
of gene trees.
- Adds new dataset SuperTreeEx for SuperTree and flatdendrapply
examples.
Changes in version 1.9.13
- SelectByK function argument ClusterSelect switched to ClusterScalar.
Cluster number selection now performed by fitting sum of total
within cluster sum of squares to a right hyperbola and taking the
ceiling of the half-max. Scalar allows a user to pick different
tolerances to select more, or less clusters. Plotting behavior
updated.
Changes in version 1.9.12
- simMat class now supports empty indexing (s[])
- simMat class now supports logical accession (s[c(T,F,T),])
Changes in version 1.9.11
- Added the function SelectByK that allows for quick removal of false
positive predicted pairs based on a relatively simple k-means
approach. Function is currently designed for use on the single
genome-to-genome pairwise comparison, and not on an all-vs-all many
genomes scale, though it may provide acceptable results on that
scale.
Changes in version 1.9.10
- New simMat class for dist-like similarity matrices that can be
manipulated like base matrices
- Major update to ProtWeaver internals
- All internal calls use simMat objects whenever possible to decrease
memory footprint
- Note ContextTree and ProfDCA require matrices internally
- ProtWeb objects now inherit from simMat
- ProtWeb.show and ProtWeb.print now display predictions in a more
natural way
- GetProtWebData() deprecated; ProtWeb now inherits
as.matrix.simMat and as.data.frame.simMat
- New documentation pages for simMat class
- GetProtWebData documentation page reworked into ProtWeb
documentation file.
- Fixes new bug in Method='Hamming' introduced in SynExtend 1.9.9
Changes in version 1.9.9
- Fixes minor bug in Method='Hamming'
- Moves some code around
Changes in version 1.9.8
- Major refactor to file structure of ProtWeaver to make individual
files more manageable
- Adds new documentation files for individual prediction streams of
predict.ProtWeaver
Changes in version 1.9.7
- BlockReconciliation now returns a an object of class PairSummaries.
Changes in version 1.9.6
- Fixes an error where warnings were mistakenly output to the user
Changes in version 1.9.5
- Moves platform-specific files in src/ (originally added by mistake)
Changes in version 1.9.4
- Lots of bugfixes to ResidueMI.ProtWeaver
- predict.ProtWeaver now correctly labels rows/columns with gene
names, not numbers
- predict.ProtWeaver now correctly handles Subset arguments
- predict.ProtWeaver(..., Subset=3) will correctly predict for all
pairs involving gene 3 (or for any gene x, as long as Subset is a
length 1 character or integer vector).
Changes in version 1.9.2
- Adds residue MI method to ProtWeaver
- Various bugfixes for ProtWeaver
Changes in version 1.7.14
- Various improvements for GenRearrScen, improves consistency and
output formatting
- Major bugfix for ProtWeaver methods using dendrogram objects
- ProtWeaver now correctly guards against non-bifurcating dendrograms
in methods that expect it
Changes in version 1.7.13
- Introduces new ProtWeaver class to predict functional association of
genes from COGs or gene trees. This implements many algorithms
commonly used in the literature, such as MirrorTree and Inverse
Potts Models.
- predict(ProtWeaverObject) returns a ProtWeb class with information
on predicted associations.
- Adds BlastSeqs to run BLAST queries on sequences stored as an
XStringSet or FASTA file.
Changes in version 1.7.12
- Updates to ExtractBy function. Methods and inputs simplified and
adjusted, and significant improvements to speed.
Changes in version 1.7.11
- Updated NucleotideOverlaps to now correctly registers hits in genes
with a large degree of overlap with the immediately preceding gene.
- Fixed aberrant behavior in BlockExpansion where contigs with zero
features could cause an error in expansion attempts.
Changes in version 1.7.10
- BlockReconciliation now allows for setting either block size or mean
PID for reconciliation precedence.
Changes in version 1.7.9
- Added retention thresholds to BlockReconciliation.
Changes in version 1.7.8
- BlockExpansion cases corrected for zero added rows.
Changes in version 1.7.7
- Improvements to BlockExpansion and BlockReconciliation functions.
Changes in version 1.7.5
- Began integration of DECIPHER's ScoreAlignment function.
Changes in version 1.7.4
- Fixed a bug in PairSummaries function.
Changes in version 1.7.3
- Added BlockExpansion function.
Changes in version 1.7.2
- Adjustment in how PairSummaries handles default translation tables
and GFF derived gene calls.
Changes in version 1.7.1
- Large changes under the hood to PairSummaries.
- Failure to accurately assign neighbors in some cases should now be
fixed.
- Extraction of genomic features is now faster.
- OffSetsAllowed argument now defaults to FALSE. This argument may be
dropped in the future in favor of a more complex function
post-summary.
- Small edits to SequenceSimilarity
Changes in version 1.5.4
- Added the function SubSetPairs that allows for easy trimming of
predicted pairs based on conflicting predictions and / or prediction
statistics.
- Added the function EstimageGenomeRearrangements that generates
rearrangement scenarios of large scale genomic events using the
double cut and join model.
Changes in version 1.5.3
- Added the function SequenceSimilarity and made improvements to
runtime in DisjointSet.
Changes in version 1.4.1
- Fixed a small bug in consensus scores in PairSummaries where
features facing on different strands had their score computed
incorrectly.
Changes in version 1.3.15
- Changes to concensus score in PairSummaries.
Changes in version 1.3.14
- Major changes to the PairSummaries function and minor changes to
NucleotideOverlaps, ExtractBy, and FindSets. Adjustments to the
model that PairSummaries calls on to predict PIDs.
Changes in version 1.3.13
- ExtractBy function has been added. Allows extraction of feature
sequences into XStingSets organized by the a PairSummaries object or
the single linkage clusters implied by pairings within the
PairSummaries objects.
- DisjointSet function added to extract single linkage clusters from a
PairSummaries object.
Changes in version 1.3.12
- PairSummaries now computes 4-mer distance between predicted pairs.
Changes in version 1.3.11
- PairSummaries now returns a column titled Adjacent that provides the
number of directly adjacent neighbor pairs to a predicted pair. Gap
filling code adjusted.
- The function FindSets has been added and performs single linkage
clustering on a pairs list as represented by vectors of integers
using the Union-Find algorithm. Long term this function will have a
larger wrapper function for user ease of access but will remain
exposed.
Changes in version 1.3.10
- NucleotideOverlap now passes it's GeneCalls object forward, allowing
PairSummaries to forego inclusion of that object as an argument.
Changes in version 1.3.9
- Minor vignette and suggested package changes.
Changes in version 1.3.8
- PairSummaries now allows users to fill in specific matching gaps in
blocks of predicted pairs with the arguments AllowGaps and
OffSetsAllowed.
Changes in version 1.3.7
- Adjustments to progress bars in both PairSummaries and
NucleotideOverlap.
- PID prediction models in PairSummaries adjusted.
Changes in version 1.3.6
- Contig name matching has been implemented. Scheme expects users to
follow NCBI contig naming and gff formats, accepting contig names
from gffs directly, and removing the first whitespace and everything
thereafter from FASTA headers. Contig name matching can be disabled
if users wish, using the argument AcceptContigNames, but ensuring
that the correct contigs in GeneCalls objects are matched to the
appropriate contigs in Synteny objects are then the user's
responsibility.
Changes in version 1.3.5
- PairSummaries now translates sequences based on transl_table
attributes provided by gene calls
- PairSummaries now uses a generic model for predicting PID
- gffToDataFrame now parses out the transl_table attribute
Changes in version 1.3.2
- Minor changes to NucleotideOverlap
- Major changes to PairSummaries - can now take in objects of class
Genes build by the DECIPHER function FindGenes()
Changes in version 0.99.30
- Vignette and help files edited for clarity
Changes in version 0.99.1
- SynExtend submitted to Bioconductor
- Added function gffToDataFrame
- Added function NucleotideOverlap
- Added function PairSummaries