philliplab ViralHaplotyper issues

philliplab / ViralHaplotyper

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outfile rename

#41 ColinAnthony opened 10 years ago
0
update the long_label in get_unique_sequence_details (left pad + frequency)

#40 philliplab opened 10 years ago
9
write summarize_haplotypes (think of less problematic name) function

#39 philliplab opened 10 years ago
0
write get_representative_sequence method for the haplotype class

#38 philliplab opened 10 years ago
0
add download buttons to shiny app

#37 philliplab closed 10 years ago
0
Improve the 'single' haplotype construction method to order the unique sequence in descending order by number of copies

#36 philliplab opened 10 years ago
1
think carefully about the output data structures of get_unique_sequence_details

#35 philliplab closed 10 years ago
1
consider renaming the haplotype class

#34 philliplab opened 10 years ago
0
create the get_unique_sequence_details method for a haplotype

#33 philliplab closed 10 years ago
0
Think how to handle naming of sequences in get_unique_sequences

#32 philliplab opened 10 years ago
2
Write accessors to get the unique and all the sequences from a haplotype

#31 philliplab closed 10 years ago
1
Implement a haplotype naming scheme

#30 philliplab closed 10 years ago
0
write the get_haplotype_size method

#29 philliplab closed 10 years ago
4
refactor the haplotype constructor

#28 philliplab closed 10 years ago
0
Simplify the haplotype class

#27 philliplab closed 10 years ago
0
followup on AWS credit query

#26 philliplab closed 10 years ago
0
Add a 'plot phylogeny' method to the haplotype class

#25 philliplab opened 10 years ago
0
Add a 'compute distance matrix' method to the haplotype class

#24 philliplab closed 10 years ago
2
Expand dist_pwa to return other kinds of distances (nedit etc) and normalize and invert the score that it currently returns

#23 philliplab closed 10 years ago
1
Add a constructor that will construct a single haplotype out of number of sequences (and handle non-unique sequences approproately)

#22 philliplab closed 10 years ago
0
fix row and column names on the distance matrix returned by seq_hap_distances

#21 philliplab closed 10 years ago
1
properly manage arguments to dist_pwa with ...

#20 philliplab closed 10 years ago
1
Why is it necessary to use BiocGenerics::table() in contruct_haplotypes instead of just table()?

#19 philliplab opened 10 years ago
0
replace haplotype@sequences in seq_hap_distances with appropriate accessor method

#18 philliplab closed 10 years ago
1
Design the different distance methods for the haplotype class

#17 philliplab closed 10 years ago
0
unit tests for constructor of Haplotype

#16 philliplab closed 10 years ago
1
create a copies class instead of storing it in a list on Haplotype

#15 philliplab closed 10 years ago
1
Create a distance function that returns 0 for exact match and 1 for non-match

#14 philliplab closed 10 years ago
1
Implement the unique haplotype construction method

#13 philliplab closed 10 years ago
0
Figure out a way to run clustering algorithms on the data that includes the non-unqiue sequences (optimization problem)

#12 philliplab opened 10 years ago
0
Design a haplotype datastructure

#11 philliplab closed 10 years ago
0
Allow difference procedures to be used for computing the distances between sequences

#10 philliplab closed 10 years ago
2
Change the scope of the package. This package only works with 1 timepoint.

#9 philliplab closed 10 years ago
0
clean up the package. A lot of hacks were made to get a demo ready for more design input. Clean up the code before moving past plotting a single cluster

#8 philliplab closed 10 years ago
1
Figure out how to do access control to the pages on phillipl.sanbi.ac.za

#7 philliplab closed 10 years ago
1
Deploy ViralHaplotyper onto phillipl.sanbi.ac.za

#6 philliplab closed 10 years ago
0
Draw a phylogenetic plot of 1 cluster that can be specified as an input

#5 philliplab closed 10 years ago
1
make the number of clusters to construct a selectable input

#4 philliplab closed 10 years ago
1
Add a table that lists sequences by average distance from all other sequences

#3 philliplab closed 10 years ago
1
annotate the big phylogenetic plot with the names of the medoid sequences

#2 philliplab opened 10 years ago
0
why does count_the_counts_of_the_sequences() cause an error?

#1 philliplab closed 10 years ago
1