dartr

Importing and Analysing DArT type snp and silicodart data

https://github.com/green-striped-gecko/dartr

Science Score: 59.0%

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Low similarity (13.3%) to scientific vocabulary

Last synced: 7 months ago · JSON representation

Repository

Importing and Analysing DArT type snp and silicodart data

Basic Info

Host: GitHub
Owner: green-striped-gecko
License: gpl-3.0
Language: R
Default Branch: master
Size: 137 MB

Statistics

Stars: 34
Watchers: 9
Forks: 22
Open Issues: 22
Releases: 2

Created about 9 years ago · Last pushed about 1 year ago

Metadata Files

Readme Contributing Code of conduct Codemeta

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# `dartR` 
## An accessible genetic analysis platform for conservation, ecology and agriculture


Main repository: 
[![](https://www.r-pkg.org/badges/version/dartR?color=blue)](https://cran.r-project.org/package=dartR)
[![CRAN checks](https://cranchecks.info/badges/summary/dartR)](https://cran.r-project.org/web/checks/check_results_dartR.html)
[![R-CMD-check](https://github.com/green-striped-gecko/dartR/workflows/R-CMD-check/badge.svg)](https://github.com/green-striped-gecko/dartR/actions)
[![R-CMD-check-beta](https://github.com/green-striped-gecko/dartR/actions/workflows/R-CMD-check-beta.yaml/badge.svg?branch=beta)](https://github.com/green-striped-gecko/dartR/actions/workflows/R-CMD-check-beta.yaml)
 [![](http://cranlogs.r-pkg.org/badges/last-week/dartR?color=orange)](https://cran.r-project.org/package=dartR)


Publication:
[![](https://img.shields.io/badge/doi-10.1111/1755--0998.12745-00cccc.svg)](https://doi.org/10.1111/1755-0998.12745)
 
Zenodo: 
[![DOI](https://zenodo.org/badge/86640709.svg)](https://zenodo.org/badge/latestdoi/86640709)  


Dev repositories: 
[![R-CMD-check-dev](https://github.com/green-striped-gecko/dartR/actions/workflows/R-CMD-check-dev.yaml/badge.svg?branch=dev)](https://github.com/green-striped-gecko/dartR/actions/workflows/R-CMD-check-dev.yaml)
[![R-CMD-check-dev_Arthur](https://github.com/green-striped-gecko/dartR/actions/workflows/R-CMD-check-dev_Arthur.yaml/badge.svg?branch=dev_arthur)](https://github.com/green-striped-gecko/dartR/actions/workflows/R-CMD-check-dev_Arthur.yaml)
[![R-CMD-check-dev_Bernd](https://github.com/green-striped-gecko/dartR/actions/workflows/R-CMD-check-dev_Bernd.yaml/badge.svg?branch=dev_bernd)](https://github.com/green-striped-gecko/dartR/actions/workflows/R-CMD-check-dev_Bernd.yaml)
[![R-CMD-check-dev_Luis](https://github.com/green-striped-gecko/dartR/actions/workflows/R-CMD-check-dev_Luis.yaml/badge.svg?branch=dev_luis)](https://github.com/green-striped-gecko/dartR/actions/workflows/R-CMD-check-dev_Luis.yaml)
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## Overview

`dartR` is a user-friendly R package that delivers a variety of analyses and pipelines on the same platform, as well as excellent user support via high-quality tutorials and documentation.

`dartR` is a collaboration between the University of Canberra, CSIRO, Diversity Arrays Technology and Monash University , and is supported with funding from the ACT Priority Investment Program, CSIRO and the University of Canberra.



   

   

   

   



## Installation

`dartR` is on CRAN, so to install it simply type:

```{r, eval = FALSE}
install.packages("dartR")
```

Because of CRAN limitations, the default installation does not include all packages needed to run all the functions; hence, specialised analyses need the installation of additional packages. The following code guarantees that all necessary packages for all `dartR` analyses are set up and ready to go.

```{r, eval = FALSE}
gl.install.vanilla.dartR()
```

You can install the development version of `dartR` from GitHub with:

``` {r, eval = FALSE}
gl.install.vanilla.dartR(flavour = "dev")
```

Please consult [this installation tutorial][installation_tutorial] if you run into any problems during setup.

## Usage

`dartR` provides several functions for handling all the steps involved in genetic data analysis, from reading multiple data input formats to manipulating, filtering, exploring and analysing the data.





We use the prefix ‘gl’ in function names to acknowledge the use of the genlight object from package [adegenet][adegenet] as our input format. 

In most cases, the following term in the function name indicates a subset of functions. 

Similarly, in most cases the first function parameter (input) is the genlight object. 

For instance, you might use the code below to generate a report and then filter your data based on the percentage of missing data:

```{r, eval = FALSE}
library(dartR)
test <- platypus.gl
rep <- gl.report.callrate(test)
test_1 <- gl.filter.callrate(test)
```

## Getting started

1. Are you a R rookie? If you want to learn R and RStudio without any fuss, have a look at our [R-refresher tutorial][intro_tutorial].

2. Let's get started by reading your genetic data into `dartR`; if you have DArT data, follow [this tutorial][input_tutorial_1]; if not, follow [this one][input_tutorial_2].

3. Checking out our [data manipulation tutorial][data_tutorial] is the easiest way to get your feet wet with `dartR`.

4. [This tutorial][filtering_tutorial] will provide some pointers on how to filter your data effectively, an important step that depends on making sound threshold assessments.

5. Check out our [simulations tutorial][sim_tutorial] to learn more about our simulation model, a powerful tool for illuminating intricate evolutionary and genetic processes.

6. In more advanced topics, check our technical notes on [Genetic Distances and  their Visualization in Population Genetics][tech_note_distances] and [Fixed Difference Analysis][tech_notes_fixed_differences].

## Getting help 

1.  Google groups Q&A forum in support of users can be accessed [here][google_groups].

2. The [RStudio community][community] provides a welcoming environment in which to ask any inquiry.

3. Answers to frequently asked topics may usually be found on [Stack Overflow][so].

## Contribute 

If you want to help shape the future of `dartR`, [this tutorial][developer_tutorial] is for you.

## Citation 

Please acknowledge `dartR` if you use it in your study. Copy and paste the following code to the R console to retrieve the citation information:

```{r, eval = FALSE}
citation("dartR")
```

Check out our [articles][articles] and our [awards][awards].

Have fun working with `dartR`! 

Cheers,

Bernd, Arthur, Luis, Carlo, Olly & Diana

[intro_tutorial]: http://georges.biomatix.org/storage/app/media/uploaded-files/Tutorial_1_dartR_RStudio_Refresher_22-Dec-21.pdf
[input_tutorial_1]: http://georges.biomatix.org/storage/app/media/uploaded-files/tutorial3adartrdatastructuresandinput22-dec-21-2.pdf
[input_tutorial_2]: http://georges.biomatix.org/storage/app/media/uploaded-files/tutorial3bdartrdatastructuresandinputfromsourcesotherthandartlmagv2-2.pdf
[data_tutorial]: http://georges.biomatix.org/storage/app/media/uploaded-files/tutorial4dartrdatamanipulation22-dec-21-3.pdf
[filtering_tutorial]: http://georges.biomatix.org/storage/app/media/uploaded-files/tutorial5dartrbasicfiltering22-dec-21-2.pdf
[developer_tutorial]: http://georges.biomatix.org/storage/app/media/uploaded-files/Tutorial_0_dartR_for_the_Developer_2.0_19-Feb-22.pdf
[installation_tutorial]: https://github.com/green-striped-gecko/dartR/wiki/Installation-tutorial
[sim_tutorial]: https://github.com/green-striped-gecko/dartR/wiki/Simulations-tutorial
[google_groups]: https://groups.google.com/g/dartr?pli=1
[community]: https://community.rstudio.com/
[so]: https://stackoverflow.com/questions/tagged/r
[adegenet]: https://doi.org/10.1093/bioinformatics/btn129
[articles]: https://github.com/green-striped-gecko/dartR/wiki/dartR-team-publications
[awards]: https://github.com/green-striped-gecko/dartR/wiki/dartR-awards
[tech_note_distances]: http://georges.biomatix.org/storage/app/media/uploaded-files/TECHNICAL_NOTE_Genetic_Distance_18-Feb-22.pdf
[tech_notes_fixed_differences]: http://georges.biomatix.org/storage/app/media/uploaded-files/TechNote_fixed_difference_analysis_25-Feb-22.pdf

Owner

Name: Bernd Gruber
Login: green-striped-gecko
Kind: user

Repositories: 11
Profile: https://github.com/green-striped-gecko

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GitHub Events

Total

Issues event: 3
Watch event: 3
Issue comment event: 7
Push event: 17
Pull request event: 8
Fork event: 1

Last Year

Issues event: 3
Watch event: 3
Issue comment event: 7
Push event: 17
Pull request event: 8
Fork event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 1,559
Total Committers: 13
Avg Commits per committer: 119.923
Development Distribution Score (DDS): 0.746

Past Year

Commits: 138
Committers: 6
Avg Commits per committer: 23.0
Development Distribution Score (DDS): 0.594

Top Committers

Name	Email	Commits
Bernd.Gruber	B**r@c**u	396
arthurgeorges	g**s@a**u	302
Luis	l**s@g**m	234
luis mijangos	l**s@u**u	224
Carlo Pacioni	c**i@g**m	104
green-striped-gecko	b**r@c**u	87
luis mijangos	L**s@g**m	87
Arthur Georges	a**s@b**u	52
Bernd Gruber	b**d@y**e	47
Arthur Georges	A****s	16
Arthur.Georges	A**s@c**u	5
Carlo Pacioni (DELWP)	c**i@d**u	3
jdyen	j**n@g**m	2

Committer Domains (Top 20 + Academic)

canberra.edu.au: 3 delwp.vic.gov.au: 1 yellowgecko.de: 1 biomatix.com.au: 1 unsw.edu.au: 1 aerg.canberra.edu.au: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 24
Total pull requests: 145
Average time to close issues: 3 months
Average time to close pull requests: 1 day
Total issue authors: 19
Total pull request authors: 3
Average comments per issue: 2.25
Average comments per pull request: 0.03
Merged pull requests: 136
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 10
Average time to close issues: N/A
Average time to close pull requests: 1 day
Issue authors: 3
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 8
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

fernandabiologia (3)
AGibsonV (2)
konopinski (2)
green-striped-gecko (2)
burbrink (1)
thomasp85 (1)
stiatragul (1)
jphruska (1)
MehrabChowdhury1 (1)
jane-edgeloe (1)
zdzbinden (1)
DaniEstevezBarcia (1)
ghost (1)
rsbivand (1)
GregorDall (1)

Pull Request Authors

mijangos81 (129)
green-striped-gecko (21)
olivroy (2)

Top Labels

Issue Labels

enhancement (2) fixed - to be closed (2) bug (1)

Pull Request Labels

Dependencies

.github/workflows/R-CMD-check-beta.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-tinytex v1 composite

.github/workflows/R-CMD-check-dev.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-tinytex v1 composite

.github/workflows/R-CMD-check-dev_Arthur.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-tinytex v1 composite

.github/workflows/R-CMD-check-dev_Bernd.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-tinytex v1 composite

.github/workflows/R-CMD-check-dev_Carlo.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-tinytex v1 composite

.github/workflows/R-CMD-check-dev_Luis.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-tinytex v1 composite

.github/workflows/R-CMD-check.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-tinytex v2 composite

.github/workflows/pkgdown.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-r-dependencies v1 composite

.github/workflows/render_markdown.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-renv v1 composite

DESCRIPTION cran

R >= 3.5 depends
adegenet >= 2.0.0 depends
dartR.data * depends
dplyr * depends
ggplot2 * depends
MASS * imports
PopGenReport * imports
SNPRelate * imports
StAMPP * imports
ape * imports
crayon * imports
data.table * imports
fields * imports
foreach * imports
gridExtra * imports
methods * imports
patchwork * imports
plyr * imports
raster * imports
reshape2 * imports
shiny * imports
sp * imports
stats * imports
stringr * imports
tidyr * imports
utils * imports
vegan * imports
HardyWeinberg * suggests
RColorBrewer * suggests
Rcpp * suggests
SIBER * suggests
boot * suggests
devtools * suggests
directlabels * suggests
dismo * suggests
doParallel * suggests
expm * suggests
gdistance * suggests
gganimate * suggests
ggrepel * suggests
ggtern * suggests
ggthemes * suggests
gplots * suggests
grid * suggests
gtable * suggests
hierfstat * suggests
igraph * suggests
iterpc * suggests
knitr * suggests
label.switching * suggests
lattice * suggests
leaflet * suggests
leaflet.minicharts * suggests
maptools * suggests
markdown * suggests
mmod * suggests
networkD3 * suggests
parallel * suggests
pca3d * suggests
pegas * suggests
pheatmap * suggests
plotly * suggests
poppr * suggests
proxy * suggests
purrr * suggests
qvalue * suggests
rgl * suggests
rmarkdown * suggests
rrBLUP * suggests
scales * suggests
seqinr * suggests
shinyBS * suggests
shinyWidgets * suggests
shinyjs * suggests
shinythemes * suggests
snpStats * suggests
stringi * suggests
terra * suggests
tibble * suggests
tidyverse * suggests
vcfR * suggests
viridis * suggests
zoo * suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

dartr

Science Score: 59.0%

Repository

Basic Info

Statistics

Metadata Files

README.Rmd

Owner

CodeMeta (codemeta.json)

GitHub Events

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Last Year

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Dependencies