bcRep news

In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Changes in version 1.3.6 (2016-12-16)

BUG FIXES

 * geneUsage() & compare.geneUsage(): explained parameter 'abundance = "relative"' in 
    help file
 * compare.geneUsage(): eliminated errors
 * clones(): eliminated error for 'useJ = FALSE'

NEW FEATURES AND FUNCTIONS

 * clones.IDlist(): returns a list containing the sequence ID's (from IMGT table) and the 
    corresponding clone number

Changes in version 1.3.5 (2016-06-03)

BUG FIXES

 * geneUsage.distance(): eliminated errors
 * geneUsage() & compare.geneUsage(): eliminated errors

NEW FEATURES AND FUNCTIONS

 * sequences.mutation.base(): Added function to calculate proportions of silent mutations 
    from nucleotide A to nucleotide B. Now, the nucleotide changes of the mutated position, 
    but also the nucleotide distributions next to the mutated position (-3 to +3) can be 
    analysed.
 * plotSequencesMutationBase(): added function to plot results of sequences.mutation.base()

Changes in version 1.3.4 (2016-04-21)

BUG FIXES

 * clones(): eliminated errors

Changes in version 1.3.3 (2016-04-15)

BUG FIXES

 * clones.filterSize(): eliminated errors
 * clones.shared(): eliminated errors
 * clones.compareGeneUsage(): eliminated errors

NEW FEATURES AND FUNCTIONS

 * plotTrueDiversity(): added option to plot mean diversities
 * plotCompareTrueDiversity(): added option to plot mean diversities

Changes in version 1.3.2 (2016-03-17)

BUG FIXES

 * sequences.geneComb(): eliminated errors
 * compare.geneUsage(): eliminated errors

Changes in version 1.3 (2016-02-25)

BUG FIXES

 * readIMGT(): eliminated errors
 * clones(): eliminated error message when no clone was found
 * geneUsage(): eliminated error for JH subgroup usage

NEW FEATURES AND FUNCTIONS

 * sequences.mutation.AA() added (proportions of amino acid mutations)
 * plotSequencesMutationAA() added
 * sequences.mutation.base() added (proportions of bases around mutations)
 * plotSequencesMutationBase() added

Changes in version 1.3 (2016-02-15)

BUG FIXES

 * clones.shared(): reduced computation time and memory; copy number of CDR3 sequences 
    changed
 * sequences.mutation(): added sequence ID's

NEW FEATURES AND FUNCTIONS

 * added NEWS
 * sequences.distance() added (distance/dissimilarity measurements on sequence data)
 * geneUsage.distance() added (distance/dissimilarity measurements on gene usage data)
 * dist.PCoA() and plotDistPCoA() added (Principal coordinate analysis on distance data
    and visualization)

Changes in version 1.2.2 (2015-10-28)

BUG FIXES

  * plotClonesCopyNumber(): added parameter to plot with and without outliers 
    (clone sizes > 75\% quantile)
  * geneUsage(): Combination of gene usage and functionality didn't work for alleles before
  * sequences.geneComb(): added parallel processing option

NEW FEATURES AND FUNCTIONS

 * added Vignette
 * combineIMGT(): combines IMGT output files from different folders
 * clones.giniIndex(): calculates Gini Index of clones
 * clones.filterSize(): filters clones for their size (number, percentage)
 * clones.filterFuntionality(): filters clones for their funtionality
 * clones.filterJunctionFrame(): filters clones for their junction frame usage
 * compare.aaDistribution(), plotCompareAADistribution(): compare amino acid distribution 
    of different samples
 * compare.trueDiversity(), plotCompareTrueDiversity(): compare richness and diversity of 
    different samples
 * compare.geneUsage(), plotCompareGeneUsage(): compare gene usage of different samples 
    (subgroup, gene, allele)

Version 1.0 (2015-10-09)

bcRep documentation built on May 2, 2019, 5:14 a.m.