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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
#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
#95: calcJunctionAlignment needs an example
task minor resolved
#87: writeChangeoDb() puts NA for null/blank values
bug minor invalid
#84: Help understanding diversity tests at a fixed diversity order
proposal major resolved
#77: (Commit hash 948e415) CLONE fields in Diversity.R need to be hard-coded and simplified
enhancement minor closed
#79: Issue is plotting output from estimateAbundance function using ExampleDb dataset
bug minor resolved
#76: Document use of collapseDuplicates outside of makeChangeClone
enhancement major new
#72: Replace gridPlot with cowplot:plot_grid
enhancement minor new
#67: changing tmp directory buildPhylipLineage
bug minor resolved
#63: Clarification to using indirect=TRUE in testEdges
bug minor resolved
#59: Add an option to aminoAcidProperties to use region definitions
proposal minor wontfix
#57: readChangeoDb reads a list of files in parallel
proposal minor invalid
#58: add `fields` to writeChangeoDb to split a db file into multiple files
proposal minor invalid
#56: `readChangeoDb` fails when input file contains non-standard column names
bug minor resolved
#54: Adding indel support to buildPhylipLineage
proposal major resolved
#51: readChangeoDb failed in sbatch mode on Farnam
bug minor resolved
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