From 2f98a892392b475fad15aa4ea64d4b5dcd16d95b Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Sun, 7 Apr 2024 00:53:57 +0000 Subject: [PATCH] Built site for RNAsum: 0.6.5@d0e97da - see https://umccr.github.io/RNAsum/ --- 404.html | 2 +- CODE_OF_CONDUCT.html | 140 ++++++++++++++++++ CONTRIBUTING.html | 103 +++++++++++++ LICENSE-text.html | 2 +- LICENSE.html | 2 +- articles/development.html | 4 +- articles/index.html | 2 +- articles/report_structure.html | 4 +- articles/tcga_projects_summary.html | 4 +- articles/workflow.html | 4 +- authors.html | 2 +- index.html | 9 +- pkgdown.yml | 2 +- reference/CapStr.html | 2 +- reference/REFERENCE_DATASETS.html | 2 +- reference/RNAsum-package.html | 2 +- reference/arriba_pdf_read.html | 10 +- reference/arriba_process.html | 2 +- reference/arriba_summary_write.html | 2 +- reference/arriba_tsv_read.html | 2 +- reference/barPlot.html | 2 +- reference/cdfPlot.html | 2 +- reference/civicDrugTable.html | 2 +- reference/cn_subset.html | 2 +- reference/combineDatasets.html | 2 +- reference/cumsum_ordered.html | 2 +- reference/densityPlot.html | 2 +- reference/dragen_fusions_process.html | 2 +- reference/dragen_fusions_read.html | 2 +- reference/dragen_mapping_metrics_read.html | 2 +- reference/empty_tbl.html | 2 +- reference/exprGroupStats_groupWise.html | 2 +- reference/exprGroupsStats_geneWise.html | 2 +- reference/exprTable.html | 2 +- reference/fusions_annot.html | 2 +- reference/fusions_preprocess.html | 2 +- reference/fusions_summary.html | 2 +- reference/fusions_table.html | 2 +- reference/genes_pcgr_summary.html | 2 +- reference/getColours.html | 2 +- reference/get_refdata.html | 2 +- reference/get_refgenes.html | 2 +- reference/glanceExprPlot.html | 2 +- reference/immune_summary.html | 2 +- reference/index.html | 2 +- reference/known_trans.html | 2 +- .../known_translocations_cgi_process.html | 2 +- reference/manta_process.html | 2 +- reference/mutCNexprPlot.html | 2 +- reference/nearest_position.html | 2 +- reference/pca.html | 2 +- reference/pcgr_expr.html | 2 +- reference/pcgr_tiers_tsv_read.html | 2 +- reference/perc_rank.html | 2 +- reference/ppl_cnv_som_gene_read.html | 2 +- reference/prepare2write.html | 2 +- reference/purple_cnv_summary.html | 2 +- reference/rcircos_cyto_info38.html | 2 +- reference/rcircos_plot.html | 2 +- reference/read_sample_data.html | 2 +- reference/read_wgs_data.html | 2 +- reference/rnasum_rmd.html | 2 +- reference/salmon_counts.html | 2 +- reference/saveWidgetFix.html | 2 +- reference/session_info_kable.html | 2 +- reference/session_info_tbls.html | 2 +- reference/sv_manta_summary.html | 2 +- reference/tidyeval.html | 2 +- reference/tpm_from_rpkm.html | 2 +- reference/webplot.html | 2 +- search.json | 2 +- sitemap.xml | 6 + 72 files changed, 333 insertions(+), 77 deletions(-) create mode 100644 CODE_OF_CONDUCT.html create mode 100644 CONTRIBUTING.html diff --git a/404.html b/404.html index bb5e03b6..88ac2589 100644 --- a/404.html +++ b/404.html @@ -24,7 +24,7 @@ RNAsum - 0.6.4 + 0.6.5 + + + + + +
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Contributor Covenant Code of Conduct

+ Source: CODE_OF_CONDUCT.md +
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Our Pledge

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We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.

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We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.

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Our Standards

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Examples of behavior that contributes to a positive environment for our community include:

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  • Demonstrating empathy and kindness toward other people
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  • Being respectful of differing opinions, viewpoints, and experiences
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  • Giving and gracefully accepting constructive feedback
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  • Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
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  • Focusing on what is best not just for us as individuals, but for the overall community
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Examples of unacceptable behavior include:

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  • The use of sexualized language or imagery, and sexual attention or advances of any kind
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  • Trolling, insulting or derogatory comments, and personal or political attacks
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  • Public or private harassment
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  • Publishing others’ private information, such as a physical or email address, without their explicit permission
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  • Other conduct which could reasonably be considered inappropriate in a professional setting
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Enforcement Responsibilities

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Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.

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Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.

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Scope

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This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.

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Enforcement

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Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at . All complaints will be reviewed and investigated promptly and fairly.

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All community leaders are obligated to respect the privacy and security of the reporter of any incident.

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Enforcement Guidelines

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Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:

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1. Correction

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Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.

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Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.

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2. Warning

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Community Impact: A violation through a single incident or series of actions.

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Consequence: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.

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3. Temporary Ban

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Community Impact: A serious violation of community standards, including sustained inappropriate behavior.

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Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.

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4. Permanent Ban

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Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.

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Consequence: A permanent ban from any sort of public interaction within the community.

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Attribution

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This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.

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Community Impact Guidelines were inspired by [Mozilla’s code of conduct enforcement ladder][https://github.com/mozilla/inclusion].

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For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. Translations are available at https://www.contributor-covenant.org/translations.

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Developed by Sehrish Kanwal, Jacek Marzec.

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Site built with pkgdown 2.0.7.

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+ + + + + + + diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html new file mode 100644 index 00000000..78f04193 --- /dev/null +++ b/CONTRIBUTING.html @@ -0,0 +1,103 @@ + +Contributing to RNAsum • RNAsum + Skip to contents + + +
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+

Contributing to RNAsum

+ Source: .github/CONTRIBUTING.md +
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+ +

This outlines how to propose a change to RNAsum. For a detailed discussion on contributing to this and other packages, please see the development contributing guide and code review principles from the tidyverse team.

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Fixing typos

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You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the source file. This generally means you’ll need to edit roxygen2 comments in an .R, not a .Rd file. You can find the .R file that generates the .Rd by reading the comment in the first line.

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Bigger changes

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If you want to make a bigger change, it’s a good idea to first file an issue and make sure someone from the team agrees that it’s needed. If you’ve found a bug, please file an issue that illustrates the bug with a minimal reprex (this will also help you write a unit test, if needed). See the tidyverse guide on how to create a great issue for more advice.

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Pull request process

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  • Fork the package and clone onto your computer. If you haven’t done this before, we recommend using usethis::create_from_github("umccr/RNAsum", fork = TRUE).

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  • Install all development dependencies with devtools::install_dev_deps(), and then make sure the package passes R CMD check by running devtools::check(). If R CMD check doesn’t pass cleanly, it’s a good idea to ask for help before continuing.

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  • Create a Git branch for your pull request (PR). We recommend using usethis::pr_init("brief-description-of-change").

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  • Make your changes, commit to git, and then create a PR by running usethis::pr_push(), and following the prompts in your browser. The title of your PR should briefly describe the change. The body of your PR should contain Fixes #issue-number.

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  • For user-facing changes, add a bullet to the top of NEWS.md (i.e. just below the first header). Follow the style described in https://style.tidyverse.org/news.html.

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Code style

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  • New code should follow the tidyverse style guide. You can use the styler package to apply these styles, but please don’t restyle code that has nothing to do with your PR.

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  • We use roxygen2, with Markdown syntax, for documentation.

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  • We use testthat for unit tests. Contributions with test cases included are easier to accept.

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Code of Conduct

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Please note that the RNAsum project is released with a Contributor Code of Conduct. By contributing to this project you agree to abide by its terms.

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Developed by Sehrish Kanwal, Jacek Marzec.

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Site built with pkgdown 2.0.7.

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+ + + + + + + diff --git a/LICENSE-text.html b/LICENSE-text.html index e1767d3a..1bf07edd 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -10,7 +10,7 @@ RNAsum - 0.6.4 + 0.6.5