Arcadia-Science sourmashconsumr issues

Arcadia-Science / sourmashconsumr

Working with the outputs of sourmash in R

https://arcadia-science.github.io/sourmashconsumr/

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Add functions to transform from sourmash taxonomy annotate outputs to phyloseq object

#27 taylorreiter closed 2 years ago
1
Add Codecov integration to CI workflow

#26 taylorreiter closed 2 years ago
1
example of making rarefaction curves from signatures representing fastq files

#25 taylorreiter closed 2 years ago
1
Add CI workflows for standard checks, linting, and test coverage

#24 taylorreiter closed 2 years ago
3
Functions to plot the output of `sourmash taxonomy annotate`

#23 taylorreiter closed 2 years ago
1
update names in metacoder function to be more consistent and clear

#22 taylorreiter closed 2 years ago
0
Change some variable names in R/metacoder.R

#21 taylorreiter closed 2 years ago
1
for `read_gather` and `read_taxonomy_annotate`, figure out how to set column type by column name

#20 taylorreiter closed 2 years ago
2
document rules for naming functions

#19 taylorreiter closed 1 year ago
3
make a vignette per sourmash output type

#18 taylorreiter closed 2 years ago
1
Add functions to produce upset plots and rarefaction plots from sourmash signatures

#17 taylorreiter closed 2 years ago
0
Create function to read sourmash signatures into functions

#16 taylorreiter closed 2 years ago
1
switch some packages that are Imported (e.g. must be installed) to Suggests (can install and load the library if suggested packages aren't installed)

#15 taylorreiter opened 2 years ago
0
add functions for rarefaction for groups of signatures using vegan

#14 taylorreiter closed 2 years ago
2
add functions to visualize and interrogate overall taxonomy results

#13 taylorreiter closed 2 years ago
3
small PR to change the name of the package from sourmashRutils to sourmashconsumr

#12 taylorreiter closed 2 years ago
1
Remove if statements associated with package loading

#11 taylorreiter closed 2 years ago
0
Set up CI and document development environment and how to develop

#10 taylorreiter closed 1 year ago
5
Add functions to plot the output of `sourmash compare`

#9 taylorreiter closed 2 years ago
0
create a function to import a sourmash taxonomy annotate file or tibble into a metacoder object

#8 taylorreiter closed 2 years ago
1
add a sankey diagram as an overview of taxonomy

#7 taylorreiter closed 2 years ago
1
package name: change to something that makes it clear that this package doesn't encode the sourmash functionality in R, but consumes the outputs of sourmash and does stuff to them

#6 taylorreiter closed 2 years ago
2
Add functions to read in outputs generated by sourmash

#5 taylorreiter closed 2 years ago
0
functions to read the outputs of sourmash

#4 taylorreiter closed 2 years ago
4
add functions for importing output of `sourmash taxonomy annotate` to phyloseq object

#3 taylorreiter closed 2 years ago
2
Add default packaging info

#1 taylorreiter closed 2 years ago
0
Functions for importing output of `sourmash taxonomy annotate` into metacoder object

#2 taylorreiter closed 2 years ago
1