bomeara/sleq issues and pull requests

#42 - Create unit tests for the ConvertNCBINodesToTree() and related functions

Issue - State: open - Opened by bomeara over 8 years ago
Labels: someday

#41 - Updating/Improving Alignment Sliding Window

Issue - State: open - Opened by kmassana over 8 years ago

#40 - Regularize SingleTaxonCompare.R

Issue - State: closed - Opened by bomeara over 8 years ago - 1 comment

#39 - be phlawd 2.0

Issue - State: open - Opened by bomeara almost 9 years ago - 2 comments
Labels: enhancement

#38 - Add SingleTaxonCompare file

Pull Request - State: closed - Opened by roszenil about 9 years ago

#37 - Removing sites from seqalignment class

Issue - State: open - Opened by thej022214 about 9 years ago - 1 comment
Labels: someday

#36 - overload rownames from seqaligment to return taxon names

Issue - State: open - Opened by bomeara about 9 years ago
Labels: someday

#35 - overload dim for seqalignment

Issue - State: closed - Opened by bomeara about 9 years ago

#34 - type vector for seqalignment

Issue - State: closed - Opened by bomeara about 9 years ago

#34 - type vector for seqalignment

Issue - State: closed - Opened by bomeara about 9 years ago

#33 - pos vector

Issue - State: closed - Opened by bomeara about 9 years ago

#32 - Subset alignment object with gene and other info

Issue - State: open - Opened by bomeara about 9 years ago

#31 - Compare your alignment with an existing alignment (from, say, treebase, or from a diff alignment program)

Issue - State: open - Opened by bomeara about 9 years ago - 1 comment

#31 - Compare your alignment with an existing alignment (from, say, treebase, or from a diff alignment program)

Issue - State: open - Opened by bomeara about 9 years ago - 1 comment

#30 - Being able to filter alignment based on annotations

Issue - State: closed - Opened by bomeara about 9 years ago - 1 comment

#29 - Deal with heterozygosity

Issue - State: open - Opened by bomeara about 9 years ago
Labels: enhancement

#29 - Deal with heterozygosity

Issue - State: open - Opened by bomeara about 9 years ago
Labels: enhancement

#28 - Keep track of number of identical seqs

Issue - State: closed - Opened by bomeara about 9 years ago - 1 comment

#27 - Deleting identical sequences

Issue - State: closed - Opened by bomeara about 9 years ago - 1 comment

#26 - Measures of alignment quality

Issue - State: open - Opened by bomeara about 9 years ago

#25 - Filter seqs for those of a certain type (i.e., all protein coding sites only)

Issue - State: open - Opened by bomeara about 9 years ago

#24 - Figure out gene function (opsin, whatever) by querying database

Issue - State: open - Opened by bomeara about 9 years ago

#23 - go from aa alignment, with unaligned nuc, to aligned nuc

Issue - State: open - Opened by bomeara about 9 years ago

#22 - Show translated aa associated with dna

Issue - State: open - Opened by bomeara about 9 years ago

#21 - Interface to short read archive

Issue - State: open - Opened by bomeara about 9 years ago

#20 - Check for contamination/mislabel by blasting

Issue - State: open - Opened by bomeara about 9 years ago

#19 - Option to highlight mismatches only in birds eye view

Issue - State: open - Opened by bomeara about 9 years ago

#18 - Consensus by species (multiple reads for one species)

Issue - State: open - Opened by bomeara about 9 years ago

#17 - Measures of sequence quality

Issue - State: open - Opened by bomeara about 9 years ago

#16 - Flag unusually long branches for inspection: maybe missing data, bad alignment

Issue - State: open - Opened by bomeara about 9 years ago

#15 - Bob Thomson function on pruning badness

Issue - State: open - Opened by bomeara about 9 years ago

#14 - next gen sequence handling (fastq, etc.)

Issue - State: open - Opened by bomeara about 9 years ago

#13 - Fix geiger code for r8s and treepl

Issue - State: closed - Opened by bomeara about 9 years ago - 1 comment

#12 - Filter for best sequence from a species (length, gaps, uncertainties)

Issue - State: open - Opened by bomeara about 9 years ago - 1 comment

#11 - phlawd in R. That you can install.

Issue - State: closed - Opened by bomeara about 9 years ago - 1 comment

#10 - Infer codon position: minimum stop codons (like Mesquite)

Issue - State: open - Opened by bomeara about 9 years ago - 1 comment

#9 - Sanderson Maximum defining label set (avoiding terrace)

Issue - State: open - Opened by bomeara about 9 years ago

#8 - Make it easy to parallelize cleaning or other fns

Issue - State: open - Opened by bomeara about 9 years ago

#7 - Sliding window for fastq quality scores

Issue - State: open - Opened by bomeara about 9 years ago

#6 - Concatenate sequences

Issue - State: closed - Opened by bomeara about 9 years ago - 1 comment

#5 - Filter bad taxa

Issue - State: closed - Opened by bomeara about 9 years ago - 1 comment

#4 - Filter for bad alignment

Issue - State: open - Opened by bomeara about 9 years ago

#3 - Split DNA at defined places

Issue - State: open - Opened by kmassana about 9 years ago

#2 - Class for sequences

Issue - State: closed - Opened by bomeara about 9 years ago
Labels: enhancement

#1 - Make CreateBirdsEyeView deal better with color

Issue - State: open - Opened by bomeara about 9 years ago
Labels: enhancement

GitHub / bomeara/sleq issues and pull requests