flowPloidy
An R package for flow cytometry histogram analysis
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
○codemeta.json file
-
○.zenodo.json file
-
○DOI references
-
○Academic publication links
-
✓Committers with academic emails
1 of 12 committers (8.3%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (14.2%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
An R package for flow cytometry histogram analysis
Statistics
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
Introduction
A tutorial overview of flowPloidy is available on
the
Bioconductor website.
This vignette is provided with the package, so once you have flowPloidy
installed you can access it from with R (see below).
Installation
Stable Version
flowPloidy is available in Bioconductor.
To install it, you need to install the bioconductor R package (more
details on the Bioconductor site ):
```{r}
try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install() ```
Once that's installed, you can install flowPloidy using the Bioconductor
tools:
{r}
BiocManager::install("flowPloidy")
BiocManager::install("flowPloidyData") # (optional) data for the examples
This should pull in all the package dependencies for flowPloidy, after
which you can load the package with the normal function
library("flowPloidy").
Development Version
To install the development version, use the following code:
```{r}
Install Bioconductor tools first:
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install()
Install flowCore from Bioconductor:
BiocManager::install("flowCore")
Install devtools so you can directly access GitHub
install.packages(devtools) library(devtools)
Install flowPloidy:
installgithub("plantarum/flowPloidy", dependencies = TRUE, buildvignettes = TRUE) ```
If the last command fails, particularly with complaints about building a
vignette, or reference to Pandoc, try with build_vignettes = FALSE
instead.
Note that I haven't yet updated the documentation to describe the
endopolyploidy analysis. To use the endopolyploidy workflow, you need to
use g2 = FALSE in your call to FlowHist or batchFlowHist. This
excludes the g2 peaks from peak fitting, treating each peak as an
independent group of cells. You may also want to increase the samples
argument to match the number of peaks; however, you can correct this in
browseFlowHist, so that's not critical.
```{r }
loading files for endopolyploidy analysis:
batch1 <- batchFlowHist(endo_files, channel="FL3.INT.LIN", g2 = FALSE, samples = 5)
batch1 <- browseFlowHist(batch1) ```
Expanding flowPloidy to handle up to six peaks (and now potentially an
unlimited number if needed) required reworking a bunch of the existing
code, and as part of this the column headings in the tables produced by
tabulateFlowHist are now different from the previous release.
Getting Started
{r}
library("flowPloidy")
The flowPloidy workflow is documented in the vignette, which you can view
from R:
{r}
fpVig <- vignette("flowPloidy-overview")
fpVig ## open vignette in a browser
edit(name = fpVig) ## open vignette source code in a text editor
It is also available online.
Getting Help
For general help using the package, you can post questions on
the Bioconductor Support Site. Use the
tag flowploidy to ensure your question is brought to my attention.
The development repository for flowPloidy is
on Github, and you can file bugs
there using the issues tab. You are also welcome to contribute features
or bug-fixes via pull requests!
Owner
- Name: Tyler Smith
- Login: plantarum
- Kind: user
- Website: http://plantarum.ca
- Repositories: 84
- Profile: https://github.com/plantarum
GitHub Events
Total
Last Year
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Tyler Smith | t****r@p****a | 130 |
| Nitesh Turaga | n****a@g****m | 14 |
| smithty | s****y@O****a | 4 |
| Herve Pages | h****s@f****g | 4 |
| Tyler Smith | p****m | 3 |
| Hervé Pagès | h****s@f****g | 2 |
| J Wokaty | j****y@s****u | 2 |
| Martin Morgan | m****n@f****g | 2 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| LiNk-NY | m****9@g****m | 1 |
| Daniel Van Twisk | d****k@r****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 5
- Total pull requests: 0
- Average time to close issues: about 1 year
- Average time to close pull requests: N/A
- Total issue authors: 5
- Total pull request authors: 0
- Average comments per issue: 7.2
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- taprs (1)
- IrisvdP (1)
- bmreilly (1)
- alex-rapp (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 14,620 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: flowPloidy
Analyze flow cytometer data to determine sample ploidy
- Homepage: https://github.com/plantarum/flowPloidy
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/flowPloidy/inst/doc/flowPloidy.pdf
- License: GPL-3
-
Latest release: 1.34.0
published 10 months ago