67 research outputs found
kelly-sovacool/tiger_salamander_project: Version 0.0.1
No full textSNP pipeline using Snakemake for the Weisrock Lab's Tiger Salamander project
TRANQUIL: TRna AbundaNce QUantification pIpeLine
No full text<ul>
<li>Now using a changelog to track user-facing changes.</li>
<li>Add a <code>mimseq_flags</code> option to the config file with <code>--local-modomics</code> set so users can customize mimseq flags. (#5, @kelly-sovacool)</li>
<li>Use a Docker container built from a <a href="https://github.com/CCBR/mim-tRNAseq/tree/docker_v1.1.8">custom fork</a> of mimseq v1.1.8. (#5, @kelly-sovacool)</li>
<li>Use upgraded singularity and snakemake modules on FRCE. (#5, @kelly-sovacool)</li>
<li>Get the pipeline version from a version file rather than git commit hash. (#7, @kelly-sovacool)</li>
</ul>
TRANQUIL: TRna AbundaNce QUantification pIpeLine
No full text<ul>
<li>Redirect the website to the README. (#8, @kelly-sovacool)</li>
<li>Use our custom installation of Python and Snakemake when running the pipeline with SLURM on FRCE. (#9, @kelly-sovacool)</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/CCBR/TRANQUIL/compare/v0.2.0...v0.2.2</p>Please cite TRANQUIL as below
TRANQUIL: TRna AbundaNce QUantification pIpeLine
No full text<ul>
<li>Redirect the website to the README. (#8, @kelly-sovacool)</li>
<li>Use our custom installation of Python and Snakemake when running the pipeline with SLURM on FRCE. (#9, @kelly-sovacool)</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/CCBR/TRANQUIL/compare/v0.2.0...v0.2.1</p>Please cite TRANQUIL as below
RENEE: Rna sEquencing aNalysis pipElinE
No full text<ul>
<li>Minor documentation improvements. (#100, @kelly-sovacool)</li>
<li>Fix RNA report bug, caused by hard-coding of PC1-3, when only PC1-2 were generated. (#104, @slsevilla)</li>
<li>Allow printing the version or help message even if singularity is not in the path. (#110, @kelly-sovacool)</li>
<li>Fix RSeQC environments:<ul>
<li>Set RSeQC envmodule version to 4.0.0, which synchronizes it with the version in the docker container used by singularity. (#122, @kelly-sovacool)</li>
<li>Update docker with RSeQC's tools properly added to the path. (#123, @kelly-sovacool)</li>
</ul>
</li>
</ul>Please cite RENEE as below
SchlossLab/mikropml-snakemake-workflow: v1.3.0
No full text<p>What's Changed</p>
<ul>
<li>Plot ROC & PRC curves by @kelly-sovacool in <a href="https://github.com/SchlossLab/mikropml-snakemake-workflow/pull/34">https://github.com/SchlossLab/mikropml-snakemake-workflow/pull/34</a></li>
<li>Create demo of running the workflow on a larger github-actions runner by @kelly-sovacool in <a href="https://github.com/SchlossLab/mikropml-snakemake-workflow/pull/38">https://github.com/SchlossLab/mikropml-snakemake-workflow/pull/38</a></li>
<li>Create otu-micro dataset for blazin' fast tests ️ by @kelly-sovacool in <a href="https://github.com/SchlossLab/mikropml-snakemake-workflow/pull/39">https://github.com/SchlossLab/mikropml-snakemake-workflow/pull/39</a></li>
<li>Improve report & ROC / PRC plots by @kelly-sovacool in <a href="https://github.com/SchlossLab/mikropml-snakemake-workflow/pull/41">https://github.com/SchlossLab/mikropml-snakemake-workflow/pull/41</a></li>
<li>Add community docs by @kelly-sovacool in <a href="https://github.com/SchlossLab/mikropml-snakemake-workflow/pull/42">https://github.com/SchlossLab/mikropml-snakemake-workflow/pull/42</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/SchlossLab/mikropml-snakemake-workflow/compare/v1.2.0...v1.3.0">https://github.com/SchlossLab/mikropml-snakemake-workflow/compare/v1.2.0...v1.3.0</a></p>
SchlossLab/schtools: schtools 0.2.1
No full textImprovements to parse_tax() (#32, @kelly-sovacool)
New column label_html provides HTML to correctly italicize genus names but not OTU labels.
Added an example to the intro vignette to demonstrate using this feature with ggtext.
Changed taxonomy data frame column names to lowercase and reordered them.
Minor documentation improvements (#33, @kelly-sovacool)
Full Changelog: https://github.com/SchlossLab/schtools/compare/v0.1.1...v0.2.
SchlossLab/mikropml: mikropml 1.1.1
No full textFixed bugs related to grouping correlated features (#276, @kelly-sovacool).
Also, group_correlated_features() is now a user-facing function
UMCarpentries/intro-curriculum-r: v1.0.0
No full textThe paper describing this curriculum will soon be published in JOSE!
What's Changed
Add instructions to create GitHub PAT by @MrFlick in https://github.com/UMCarpentries/intro-curriculum-r/pull/145
Typos and other minor corrections by @kdillmcfarland in https://github.com/UMCarpentries/intro-curriculum-r/pull/151
Update setup.md by @kdillmcfarland in https://github.com/UMCarpentries/intro-curriculum-r/pull/146
Include overview summary on index page by @zenalapp in https://github.com/UMCarpentries/intro-curriculum-r/pull/153
Update install instructions by @zenalapp in https://github.com/UMCarpentries/intro-curriculum-r/pull/155
Fix broken links by @kelly-sovacool in https://github.com/UMCarpentries/intro-curriculum-r/pull/156
Update GitHub Actions & related code from the carpentries/styles repo by @kelly-sovacool in https://github.com/UMCarpentries/intro-curriculum-r/pull/157
JOSE submission suggestions by @zenalapp in https://github.com/UMCarpentries/intro-curriculum-r/pull/159
Incorporate JOSE feedback in Git/GitHub lesson by @kelly-sovacool in https://github.com/UMCarpentries/intro-curriculum-r/pull/158
Use the carpentries/styles website build workflow by @kelly-sovacool in https://github.com/UMCarpentries/intro-curriculum-r/pull/160
Minor edits by @zenalapp in https://github.com/UMCarpentries/intro-curriculum-r/pull/163
Fix callout boxes & comment-out glossary in Git/GitHub by @kelly-sovacool in https://github.com/UMCarpentries/intro-curriculum-r/pull/164
Fix formatting in R for Plotting by @kelly-sovacool in https://github.com/UMCarpentries/intro-curriculum-r/pull/162
Beautify the README with badges by @kelly-sovacool in https://github.com/UMCarpentries/intro-curriculum-r/pull/165
Auto-detect broken links with GitHub Actions by @kelly-sovacool in https://github.com/UMCarpentries/intro-curriculum-r/pull/154
Better broken link detection by @MrFlick in https://github.com/UMCarpentries/intro-curriculum-r/pull/166
Suggesting changes to CoC guidelines language by @tracykteal in https://github.com/UMCarpentries/intro-curriculum-r/pull/169
Clarify our connection to The Carpentries by @kelly-sovacool in https://github.com/UMCarpentries/intro-curriculum-r/pull/171
New Contributors
@kdillmcfarland made their first contribution in https://github.com/UMCarpentries/intro-curriculum-r/pull/151
@tracykteal made their first contribution in https://github.com/UMCarpentries/intro-curriculum-r/pull/169
Full Changelog: https://github.com/UMCarpentries/intro-curriculum-r/compare/v0.1.0...v1.0.
SchlossLab/mikropml: mikropml 1.2.0
No full textNew parameter cross_val added to run_ml() allows users to define their own custom cross-validation scheme (#278, @kelly-sovacool).
Also added a new parameter calculate_performance, which controls whether performance metrics are calculated (default: TRUE). Users may wish to skip performance calculations when training models with no cross-validation.
New parameter group_partitions added to run_ml() allows users to control which groups should go to which partition of the train/test split (#281, @kelly-sovacool).
Modified the training_frac parameter in run_ml() (#281, @kelly-sovacool).
By default, training_frac is a fraction between 0 and 1 that specifies how much of the dataset should be used in the training fraction of the train/test split.
Users can instead give training_frac a vector of indices that correspond to which rows of the dataset should go in the training fraction of the train/test split. This gives users direct control over exactly which observations are in the training fraction if desired
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