Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: jtlandis
- License: other
- Language: R
- Default Branch: devel
- Homepage: https://jtlandis.github.io/plyxp/
- Size: 24.6 MB
Statistics
- Stars: 4
- Watchers: 1
- Forks: 0
- Open Issues: 5
- Releases: 0
Metadata Files
README.md
plyxp
plyxp provides efficient abstractions to SummarizedExperiment such
that using common dplyr functions feels as natural to operating on a
data.frame or tibble.
plyxp makes use of a concise grammar for exploring and manipulating annotated
matrix data in the form of the SummarizedExperiment, scaling from simple to
complex operations spanning one or more tables of data.
We also aim for optimized implementations in plyxp to power some functionality
within the tidySummarizedExperiment package, which also offers a dplyr-like
interface to SummarizedExperiment. These two packages can easily be used in
parallel, by casting objects with the new_plyxp constructor to enable
plyxp-driven functionality.
plyxp uses
data-masking
from the rlang package in order to connect dplyr functions to
SummarizedExperiment slots in a manner that aims to be intuitive and avoiding
ambiguity in outcomes.
Note: This package is still under active development. Feel free to reach out to the package developers, see Feedback section below.
installing plyxp
```r
plyxp is available on BiocManager version 3.20
BiocManager::install("plyxp") ```
data masking SummarizedExperiment
\
The SummarizedExperiment object contains three main components/"contexts" that we mask,
the assays(), rowData()[^1] and colData().
[^1]: At this moment rowRanges() is not supported in plyxp but may become
its own pronoun in the future.
](man/figures/Overview-bindings.png)
\
plyxp provides variables as-is to data within their current contexts enabling you
to call S4 methods on S4 objects with dplyr verbs. If you require access to
variables outside the context, you may use
pronouns made available through plyxp to specify where to find those
variables.
](man/figures/Overview-pronouns.png)
\
The .assays, .rows and .cols pronouns outputs depends on the evaluating
context. Users should expect that the underlying data returned from .rows or
.cols pronouns in the assays context is a vector, replicated to match
size of the assay context.
\
Alternatively, using a pronoun in either the rows() or cols()
contexts will likely return a list equal in length to either nrows(rowData())
or nrows(colData()) respectively.
Feedback
We would love to hear your feedback. Please post to
Bioconductor support site
or the
#tidiness_in_bioc Slack channel on community-bioc
for software usage help,
or post an
Issue on GitHub,
for software development questions.
Funding
plyxp was supported by a EOSS cycle 6 grant from The Wellcome Trust.
Owner
- Name: Justin Landis
- Login: jtlandis
- Kind: user
- Location: Chapel Hill, NC
- Repositories: 3
- Profile: https://github.com/jtlandis
Data scientist at the University of North Carolina at Chapel Hill || R developer
GitHub Events
Total
- Issues event: 6
- Watch event: 6
- Delete event: 1
- Issue comment event: 2
- Member event: 1
- Push event: 64
- Create event: 9
Last Year
- Issues event: 6
- Watch event: 6
- Delete event: 1
- Issue comment event: 2
- Member event: 1
- Push event: 64
- Create event: 9
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 6
- Total pull requests: 0
- Average time to close issues: 2 months
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 0.17
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 0
- Average time to close issues: 2 months
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 0.17
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jtlandis (5)
- sa-lee (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 2,257 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 4
- Total maintainers: 1
bioconductor.org: plyxp
Data masks for SummarizedExperiment enabling dplyr-like manipulation
- Homepage: https://github.com/jtlandis/plyxp https://jtlandis.github.io/plyxp
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/plyxp/inst/doc/plyxp.pdf
- License: MIT + file LICENSE
-
Latest release: 1.2.7
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- docker/build-push-action v1 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- R >= 4.4.0 depends
- S4Vectors * imports
- S7 * imports
- SummarizedExperiment * imports
- cli * imports
- dplyr * imports
- glue * imports
- methods * imports
- pillar * imports
- purrr * imports
- rlang * imports
- tibble * imports
- tidyr * imports
- tidyselect * imports
- utils * imports
- vctrs * imports
- IRanges * suggests
- airway * suggests
- devtools * suggests
- here * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests