iSEEfier
Making omics data visualization as effortless as watching the flames burn auburn on the mountain side 🧬🔥
Science Score: 13.0%
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â—‹Scientific vocabulary similarity
Low similarity (15.6%) to scientific vocabulary
Repository
Making omics data visualization as effortless as watching the flames burn auburn on the mountain side 🧬🔥
Basic Info
- Host: GitHub
- Owner: NajlaAbassi
- License: other
- Language: R
- Default Branch: devel
- Homepage: https://NajlaAbassi.github.io/iSEEfier
- Size: 9.87 MB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
iSEEfier
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The goal of iSEEfier is to provides a set of functionality to quickly and intuitively create,
inspect, and combine initial configuration objects for the iSEE package.
These can be conveniently passed in a straightforward manner to the function call
to launch iSEE() with the specified configuration, tailored to individual visualisation
objectives.
This package currently works seamlessly with the sets of panels provided by the
iSEE and iSEEu packages, but can be extended to accommodate the usage of any
custom panel (e.g. from iSEEde, iSEEpathways, or any panel developed independently
by the user).
iSEEfier can be found on Bioconductor
(https://www.bioconductor.org/packages/iSEEfier).
Installation
You can install the development version of iSEEfier from GitHub with:
r
library("remotes")
remotes::install_github("NajlaAbassi/iSEEfier",
dependencies = TRUE, build_vignettes = TRUE)
Example
This is a basic example which shows you how to use iSEEfier on a demo
dataset (the one included in the scRNAseq package).
``` r library(iSEEfier) library(iSEE)
sce <- scRNAseq::RichardTCellData() sce <- scuttle::logNormCounts(sce) sce <- scater::runPCA(sce) sce <- scater::runTSNE(sce)
gene_list <- c("ENSMUSG00000026581", "ENSMUSG00000005087", "ENSMUSG00000015437") cluster <- "stimulus" group <- "single cell quality"
initial <- iSEEinit(sce = sce, features = gene_list, clusters = cluster, groups = group)
iSEE(sce, initial = initial) ```
Usage overview
You can find the rendered version of the documentation of iSEEfier at
the project website https://NajlaAbassi.github.io/iSEEfier,
created with pkgdown.
Development
If you encounter a bug, have usage questions, or want to share ideas and functionality to make this package better, feel free to file an issue.
Code of Conduct
Please note that the iSEEfier project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
License
MIT
Owner
- Name: Najla Abassi
- Login: NajlaAbassi
- Kind: user
- Company: IMBEI
- Website: https://www.linkedin.com/in/najla-abassi/
- Repositories: 1
- Profile: https://github.com/NajlaAbassi
Bioinformatician/Research Assistant
GitHub Events
Total
- Push event: 6
- Pull request event: 2
- Create event: 1
Last Year
- Push event: 6
- Pull request event: 2
- Create event: 1
Issues and Pull Requests
Last synced: 12 months ago
All Time
- Total issues: 1
- Total pull requests: 9
- Average time to close issues: about 10 hours
- Average time to close pull requests: 5 days
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 1.0
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: 20 days
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 4.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- NajlaAbassi (1)
Pull Request Authors
- NajlaAbassi (8)
- federicomarini (5)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 3,534 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 3
- Total maintainers: 1
bioconductor.org: iSEEfier
Streamlining the creation of initial states for starting an iSEE instance
- Homepage: https://github.com/NajlaAbassi/iSEEfier
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/iSEEfier/inst/doc/iSEEfier.pdf
- License: MIT + file LICENSE
-
Latest release: 1.4.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/cache v1 composite
- actions/checkout v2 composite
- actions/upload-artifact main composite
- grimbough/bioc-actions/build-install-check v1 composite
- grimbough/bioc-actions/run-BiocCheck v1 composite
- grimbough/bioc-actions/setup-bioc v1 composite
- r-lib/actions/setup-pandoc v2 composite
- SummarizedExperiment * imports
- iSEE * imports
- iSEEu * imports
- methods * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests
- scRNAseq * suggests
- scater * suggests
- scuttle * suggests
- testthat >= 3.0.0 suggests