Version 0.2.5: August 5, 2016

General:

• Fixed a bug in seqDist() wherein distance was not properly calculated in some sequences containing gap characters.
• Added stop and gap characters to getAAMatrix() return matrix.

Version 0.2.4: July 20, 2016

General:

• Added Rcpp and data.table dependencies.
• Modified readChangeoDb() to wrap data.table::fread() instead of utils::read.table() if the input file is not compressed.
• Ported testSeqEqual(), getSeqDistance() and getSeqMatrix() to C++ to improve performance of collapseDuplicates() and other dependent functions.
• Renamed testSeqEqual(), getSeqDistance() and getSeqMatrix() to seqEqual(), seqDist() and pairwiseDist(), respectively.
• Added pairwiseEqual() which creates a logical sequence distance matrix; TRUE if sequences are identical, FALSE if not, excluding Ns and gaps.
• Added translation of ambiguous and gap characters to X in translateDNA().
• Fixed bug in collapseDuplicates() wherein the input data type sanity check would cause the vignette to fail to build under R 3.3.
• Replaced the ExampleDb.gz file with a larger, more clonal, ExampleDb data object.
• Replaced ExampleTrees with a larger set of trees.
• Renamed multiggplot() to gridPlot().

Amino Acid Analysis:

• Set default to normalize=FALSE for charge calculations to be more consistent with previously published repertoire sequencing results.

Diversity Analysis:

• Added a progress argument to rarefyDiversity() and testDiversity() to enable the (previously default) progress bar.
• Fixed a bug in estimateAbundance() were the function would fail if there was only a single input sequence per group.
• Changed column names in data and summary slots of DiversityTest to uppercase for consistency with other tools.
• Added dispatching of plot to plotDiversityCurve for DiversityCurve objects.

Gene Usage:

• Added sortGenes() function to sort V(D)J genes by name or locus position.
• Added clone argument to countGenes() to allow restriction of gene abundance to one gene per clone.

Topology Analysis:

• Added a set of functions for lineage tree topology analysis.
• Added a vignette showing basic tree topology analysis.

Version 0.2.3: February 22, 2016

General:

• Fixed a bug wherein the package would not build on R < 3.2.0 due to changes in base::nchar().
• Changed R dependency to R >= 3.1.2.

Version 0.2.2: January 29, 2016

General:

• Updated license from CC BY-NC-SA 3.0 to CC BY-NC-SA 4.0.
• Internal changes to conform to CRAN policies.

Amino Acid Analysis:

• Fixed bug where arguments for the aliphatic() function were not being passed through the ellipsis argument of aminoAcidProperties().
• Improved amino acid analysis vignette.
• Added check for correctness of amino acids sequences to aminoAcidProperties().
• Renamed AA_TRANS to ABBREV_AA.

Diversity:

• Added evenness and bootstrap standard deviation to rarefyDiversity() output.

Lineage:

• Added ExampleTrees data with example output from buildPhylipLineage().

Version 0.2.1: December 18, 2015

General:

• Removed plyr dependency.
• Added dplyr, lazyeval and stringi dependencies.
• Added strict requirement for igraph version >= 1.0.0.
• Renamed getDNADistMatrix() and getAADistMatrix() to getDNAMatrix and getAAMatrix(), respectively.
• Added getSeqMatrix() which calculates a pairwise distance matrix for a set of sequences.
• Modified default plot sizing to be more appropriate for export to PDF figures with 7-8 inch width.
• Added multiggplot() function for performing multiple panel plots.

Amino Acid Analysis:

• Migrated amino acid property analysis from Change-O CTL to alakazam. Includes the new functions gravy(), bulk(), aliphatic(), polar(), charge(), countPatterns() and aminoAcidProperties().

Annotation:

• Added support for unusual TCR gene names, such as 'TRGVA*01'.
• Added removal of 'D' label (gene duplication) from gene names when parsed with getSegment(), getAllele(), getGene() and getFamily(). May be disabled by providing the argument strip_d=FALSE.
• Added countGenes() to tabulate V(D)J allele, gene and family usage.

Diversity:

• Added several functions related to analysis of clone size distributions, including countClones(), estimateAbundance() and plotAbundance().
• Renamed resampleDiversity() to rarefyDiversity() and changed many of the internals. Bootstrapping is now performed on an inferred complete relative abundance distribution.
• Added support for inclusion of copy number in clone size determination within rarefyDiversity() and testDiversity().
• Diversity scores and confiderence intervals within rarefyDiversity() and testDiversity() are now calculated using the mean and standard deviation of the bootstrap realizations, rather than the median and upper/lower quantiles.
• Added ability to add counts to the legend in plotDiversityCurve().

Version 0.2.0: June 15, 2015

Initial public release.

General:

• Added citations for the citation("alakazam") command.

Version 0.2.0.beta-2015-05-30: May 30, 2015

Lineage:

• Added more error checking to buildPhylipLineage().

Version 0.2.0.beta-2015-05-26: May 26, 2015

Lineage:

• Fixed issue where buildPhylipLineage() would hang on R 3.2 due to R change request PR#15508.

Version 0.2.0.beta-2015-05-05: May 05, 2015

Prerelease for review.