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Issues (1–25 of 108)

Title T P Status Votes Assignee Milestone Created Updated Actions
#108: Using multiple columns as groups in alphaDiversity
enhancement major open
#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
#107: Missing gene usage values for genes with "D" in the name
proposal major closed
#106: change groupGenes only_heavy default from T to F
bug major new
#104: readChangeoDb convert the sequence_id column into double, probably when ID start by a digit
bug major resolved
#102: update estimateAbundance, plotAbundanceCurve to work with mixed data
enhancement major new
#101: Error running estimateAbundance
bug major resolved
#100: Clonal diversity
bug major resolved
#99: Calculate clonal frequencies
enhancement major resolved 1
#98: R CMD check is too slow for CRAN
bug blocker new
#97: Bioconductor packages don't install automatically
bug major new
#96: Use AIRR-ish names for output fields of calcJunctionAlignment
enhancement trivial resolved
#94: buildPhylipLineage fails on Windows
bug major resolved 1
#95: calcJunctionAlignment needs an example
task minor resolved
#92: Add readAIRR() and update readChangeoDb(). They should accept a vector of files and check uniqueness
proposal minor new 1
#93: Have countClones handle NAs in clone_id
enhancement trivial resolved
#88: Clarify file I/O documentation
enhancement minor resolved
#87: writeChangeoDb() puts NA for null/blank values
bug minor invalid
#85: IgPhyML lineage tree analysis does not work with test data
bug major resolved
#84: Help understanding diversity tests at a fixed diversity order
proposal major resolved
#83: groupGenes doesn't support TCR data
bug major resolved
#77: (Commit hash 948e415) CLONE fields in Diversity.R need to be hard-coded and simplified
enhancement minor closed
#81: Lower case in readIgphyml and combineIgphyml
task major resolved
#78: collapseDuplicates edge case (every sequence in a clone_id is ambiguous except for one sequence)
bug minor resolved
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