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bomeara
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sleq
A sleek package to deal with sequences in R. Joint O'Meara lab project.
GNU General Public License v2.0
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Create unit tests for the ConvertNCBINodesToTree() and related functions
#42
bomeara
opened
8 years ago
0
Updating/Improving Alignment Sliding Window
#41
kmassana
opened
8 years ago
0
Regularize SingleTaxonCompare.R
#40
bomeara
closed
8 years ago
1
be phlawd 2.0
#39
bomeara
opened
8 years ago
2
Add SingleTaxonCompare file
#38
roszenil
closed
8 years ago
0
Removing sites from seqalignment class
#37
thej022214
opened
8 years ago
1
overload rownames from seqaligment to return taxon names
#36
bomeara
opened
8 years ago
0
overload dim for seqalignment
#35
bomeara
closed
8 years ago
0
type vector for seqalignment
#34
bomeara
closed
8 years ago
0
pos vector
#33
bomeara
closed
8 years ago
0
Subset alignment object with gene and other info
#32
bomeara
opened
8 years ago
0
Compare your alignment with an existing alignment (from, say, treebase, or from a diff alignment program)
#31
bomeara
opened
8 years ago
1
Being able to filter alignment based on annotations
#30
bomeara
closed
8 years ago
1
Deal with heterozygosity
#29
bomeara
opened
8 years ago
0
Keep track of number of identical seqs
#28
bomeara
closed
8 years ago
1
Deleting identical sequences
#27
bomeara
closed
8 years ago
1
Measures of alignment quality
#26
bomeara
opened
8 years ago
0
Filter seqs for those of a certain type (i.e., all protein coding sites only)
#25
bomeara
opened
8 years ago
0
Figure out gene function (opsin, whatever) by querying database
#24
bomeara
opened
8 years ago
0
go from aa alignment, with unaligned nuc, to aligned nuc
#23
bomeara
opened
8 years ago
0
Show translated aa associated with dna
#22
bomeara
opened
8 years ago
0
Interface to short read archive
#21
bomeara
opened
8 years ago
0
Check for contamination/mislabel by blasting
#20
bomeara
opened
8 years ago
0
Option to highlight mismatches only in birds eye view
#19
bomeara
opened
8 years ago
0
Consensus by species (multiple reads for one species)
#18
bomeara
opened
8 years ago
0
Measures of sequence quality
#17
bomeara
opened
8 years ago
0
Flag unusually long branches for inspection: maybe missing data, bad alignment
#16
bomeara
opened
8 years ago
0
Bob Thomson function on pruning badness
#15
bomeara
opened
8 years ago
0
next gen sequence handling (fastq, etc.)
#14
bomeara
opened
8 years ago
0
Fix geiger code for r8s and treepl
#13
bomeara
closed
8 years ago
1
Filter for best sequence from a species (length, gaps, uncertainties)
#12
bomeara
opened
8 years ago
1
phlawd in R. That you can install.
#11
bomeara
closed
8 years ago
1
Infer codon position: minimum stop codons (like Mesquite)
#10
bomeara
opened
8 years ago
1
Sanderson Maximum defining label set (avoiding terrace)
#9
bomeara
opened
8 years ago
0
Make it easy to parallelize cleaning or other fns
#8
bomeara
opened
8 years ago
0
Sliding window for fastq quality scores
#7
bomeara
opened
8 years ago
0
Concatenate sequences
#6
bomeara
closed
8 years ago
1
Filter bad taxa
#5
bomeara
closed
8 years ago
1
Filter for bad alignment
#4
bomeara
opened
8 years ago
0
Split DNA at defined places
#3
kmassana
opened
8 years ago
0
Class for sequences
#2
bomeara
closed
8 years ago
0
Make CreateBirdsEyeView deal better with color
#1
bomeara
opened
8 years ago
0