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Issues (26–50 of 55)

Title T P Status Votes Assignee Milestone Created Updated Actions
#42: getSeqMatrix vs getDistanceMatrix
enhancement minor invalid
#39: Consider having readChangeoDb wrap fread() instead of read.table()
enhancement minor resolved
#21: Add evenness to diversity output
enhancement minor resolved
#31: R CMD Check warning
enhancement minor resolved
#17: Move amino acid analysis from repertoire into main alakazam package
enhancement minor resolved
#24: R CMD Check gravy warning
enhancement minor resolved
#23: R CMD Check igraph warning
enhancement minor resolved
#20: Parallelize diversity and abundance calculations
enhancement minor new
#7: Add cross-sample distToNearest mode
enhancement minor invalid
#4: readChangeoDb should probably convert all columns to character type
enhancement minor resolved
#8: Remove globals for default colors
enhancement minor resolved
#5: collapseDuplicates could use binary distance instead for speed
enhancement minor resolved
#103: groupGenes needs updated naming and to figure out the locus list.
bug minor resolved
#105: ylim argument in plotAbundanceCurve has no effect
bug minor resolved
#91: basic, acidic and aromatic output fields from aminoAcidProperties() are always zero
bug minor resolved
#90: NA row for geneCounts() on d_call
bug minor resolved
#89: getSegment doesn't work for C-regions
bug minor resolved
#87: writeChangeoDb() puts NA for null/blank values
bug minor invalid
#78: collapseDuplicates edge case (every sequence in a clone_id is ambiguous except for one sequence)
bug minor resolved
#80: alakazam::getnproc can sometimes return NA because of parallel::detectCores() which can be problematic for functions that use this command e.g. groupBaseline
bug minor resolved
#79: Issue is plotting output from estimateAbundance function using ExampleDb dataset
bug minor resolved
#74: Remove NSE from gather call in combineIgphyml
bug minor resolved
#70: error and warning messages from plotDiversityCurve()
bug minor resolved
#67: changing tmp directory buildPhylipLineage
bug minor resolved
#63: Clarification to using indirect=TRUE in testEdges
bug minor resolved
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