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https://github.com/kullrich/korthor
korthoR calculates pairwise kmer jaccard distance between all sequences of an AAStringSet
https://github.com/kullrich/korthor
Last synced: 4 days ago
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korthoR calculates pairwise kmer jaccard distance between all sequences of an AAStringSet
- Host: GitHub
- URL: https://github.com/kullrich/korthor
- Owner: kullrich
- License: gpl-3.0
- Created: 2024-03-01T14:48:39.000Z (8 months ago)
- Default Branch: main
- Last Pushed: 2024-03-05T07:04:23.000Z (8 months ago)
- Last Synced: 2024-03-05T14:56:24.112Z (8 months ago)
- Language: HTML
- Size: 797 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# korthoR 
`korthoR` calculates pairwise kmer jaccard distance between all sequences of an `AAStringSet`.
## Installation instructions
## R specific installation prerequisites
### install packages from [cran](https://cran.r-project.org/web/packages/index.html)
In most cases you need to first install the following system-wide packages to be able to compile the R dependencies. If you do not have 'sudo' rights, please ask your system-admin to install them for you.
Ubuntu/Debian
```
sudo apt-get install libcurl4-openssl-dev libssl-dev libxml2-dev libglu1-mesa-dev libgit2-dev
#Pandoc is required to build R Markdown vignettes
#sudo apt-get install pandoc
#pkgdown dependencies - pkgdown is used to build R package pages
#sudo apt-get install libssh2-1-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
```
CentOS
```
sudo yum install libcurl-devel openssl-devel libxml2-devel mesa-libGLU-devel libgit2-devel
#Pandoc is required to build R Markdown vignettes
#sudo yum install pandoc
#pkgdown dependencies - pkgdown is used to build R package pages
#sudo yum install libssh2-devel fontconfig-devel harfbuzz-devel fribidi-devel freetype-devel libpng-devel libtiff-devel libjpeg-turbo-devel
```
- [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html)
- [RcppThread](https://cran.r-project.org/web/packages/RcppThread/index.html)
- [devtools](https://cran.r-project.org/web/packages/devtools/index.html)
- [testthat](https://cran.r-project.org/web/packages/testthat/index.html)
- [reshape2](https://cran.r-project.org/web/packages/reshape2/index.html)
- [dplyr](https://cran.r-project.org/web/packages/dplyr/index.html)
- [ape](https://cran.r-project.org/web/packages/ape/index.html)
```
install.packages("Rcpp")
install.packages("RcppThread")
install.packages("devtools")
install.packages("testthat")
install.packages("reshape2")
install.packages("dplyr")
install.packages("ape")
```
### install packages from [Bioconductor](https://www.bioconductor.org/)
- [MSA2dist](https://bioconductor.org/packages/release/bioc/html/MSA2dist.html)
```
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(
c(
"MSA2dist")
)
```
### install [korthoR](https://github.com/kullrich/korthoR)
```
devtools::install_github("kullrich/korthoR", build_vignettes = TRUE, dependencies = TRUE)
```
## Quick-guide
```
library(korthoR)
## load example sequence data
data("hiv", package="MSA2dist")
## count kmers of length 6 for all amino acids
l <- hiv |>
MSA2dist::cds2aa() |>
korthoR::count_kmers(k=6)
l
## count kmers using multiple threads
l <- hiv |>
MSA2dist::cds2aa() |>
korthoR::count_kmers(k=6, threads=2)
l
## get jaccard distance
hiv |>
MSA2dist::cds2aa() |>
korthoR::count_kmers(k=6) |>
korthoR::get_jaccard_from_self(k=6)
## get jaccard distance using multiple threads
hiv |>
MSA2dist::cds2aa() |>
korthoR::count_kmers(k=6, threads=2) |>
korthoR::get_jaccard_from_self(k=6, threads=2)
## get bionjs tree
data(hiv, package="MSA2dist")
l <- hiv |>
MSA2dist::cds2aa() |>
korthoR::count_kmers(k=6)
d <- korthoR::get_jaccard_a_b(kmer_counts_q=l,
kmer_counts_t=l,
k=6)
t1 <- get_bionjs_tree(jaccard_df=d, value="jaccard")
t2 <- get_bionjs_tree(jaccard_df=d, value="mash")
t3 <- get_bionjs_tree(jaccard_df=d, value="sumdist")
par(mfrow=c(1,3))
plot(t1, main="jaccard")
plot(t2, main="mash")
plot(t3, main="sumdist")
```
## License
GPL-3 (see LICENSE)
## Contributing Code
If you would like to contribute to korthoR, please file an issue so that one can establish a statement of need, avoid redundant work, and track progress on your contribution.
Before you do a pull request, you should always file an issue and make sure that someone from the korthoR developer team agrees that it's a problem, and is happy with your basic proposal for fixing it.
Once an issue has been filed and we've identified how to best orient your contribution with package development as a whole, [fork](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) the [main repo](https://github.com/kullrich/korthoR.git), branch off a [feature branch](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-branches) from `main`, [commit](https://docs.github.com/en/desktop/contributing-and-collaborating-using-github-desktop/committing-and-reviewing-changes-to-your-project) and [push](https://docs.github.com/en/github/using-git/pushing-commits-to-a-remote-repository) your changes to your fork and submit a [pull request](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/proposing-changes-to-your-work-with-pull-requests) for `korthoR:main`.
By contributing to this project, you agree to abide by the Code of Conduct terms.
## Bug reports
Please report any errors or requests regarding [korthoR](https://github.com/kullrich/korthoR) to Kristian Ullrich ([email protected])
or use the issue tracker at [https://github.com/kullrich/korthoR/issues](https://github.com/kullrich/korthoR/issues)
## Code of Conduct - Participation guidelines
This repository adhere to [Contributor Covenant](https://contributor-covenant.org) code of conduct for in any interactions you have within this project. (see [Code of Conduct](https://github.com/kullrich/korthoR/-/blob/main/CODE_OF_CONDUCT.md))
See also the policy against sexualized discrimination, harassment and violence for the Max Planck Society [Code-of-Conduct](https://www.mpg.de/11961177/code-of-conduct-en.pdf).
By contributing to this project, you agree to abide by its terms.
## References
Pagès H., Aboyoun P., Gentleman R., and DebRoy S. (2017). **Biostrings: Efficient manipulation of biological strings.** *R package version*, 2.56.0. [Biostrings](http://bioconductor.org/packages/release/bioc/html/Biostrings.html)
Paradis E., Schliep K. (2019). **ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.** *Bioinformatics*, **35**, 526-528.[https://doi.org/10.1093/bioinformatics/bty633](https://doi.org/10.1093/bioinformatics/bty633)
Scrucca L., Fraley C., Murphy T.B., Raftery A.E.(2023). **Model-based clustering, classification, and density estimation using mclust in R.** *Chapman and Hall/CRC* [https://doi.org/10.1201/9781003277965](https://doi.org/10.1201/9781003277965)
Sheikhizadeh A.S., de Ridder D., Schranz M.E., Smit S. (2018). **Efficient inference of homologs in large eukaryotic pan-proteomes.** *BMC bioinformatics*,*. 2018 Dec; **19(1)**, 1-1. [https://doi.org/10.1186/s12859-018-2362-4](https://doi.org/10.1186/s12859-018-2362-4)