Nothing
* geneUsage() & compare.geneUsage(): explained parameter 'abundance = "relative"' in help file * compare.geneUsage(): eliminated errors * clones(): eliminated error for 'useJ = FALSE'
* clones.IDlist(): returns a list containing the sequence ID's (from IMGT table) and the corresponding clone number
* geneUsage.distance(): eliminated errors * geneUsage() & compare.geneUsage(): eliminated errors
* 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()
* clones(): eliminated errors
* clones.filterSize(): eliminated errors * clones.shared(): eliminated errors * clones.compareGeneUsage(): eliminated errors
* plotTrueDiversity(): added option to plot mean diversities * plotCompareTrueDiversity(): added option to plot mean diversities
* sequences.geneComb(): eliminated errors * compare.geneUsage(): eliminated errors
* readIMGT(): eliminated errors * clones(): eliminated error message when no clone was found * geneUsage(): eliminated error for JH subgroup usage
* sequences.mutation.AA() added (proportions of amino acid mutations) * plotSequencesMutationAA() added * sequences.mutation.base() added (proportions of bases around mutations) * plotSequencesMutationBase() added
* clones.shared(): reduced computation time and memory; copy number of CDR3 sequences changed * sequences.mutation(): added sequence ID's
* 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)
* 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
* 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)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.