{"id":24585915,"url":"https://github.com/j-andrews7/onelineromics","last_synced_at":"2025-06-24T23:07:03.621Z","repository":{"id":88619388,"uuid":"211183283","full_name":"j-andrews7/OneLinerOmics","owner":"j-andrews7","description":"One liner analyses and visualizations for bulk RNA-seq and ChIP-seq 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OneLinerOmics\n\n[![Docs](https://img.shields.io/badge/docs-site-brightgreen?style=plastic)](https://j-andrews7.github.io/OneLinerOmics)\n\nThis R package contains several functions that compress major RNA-seq and ChIP-seq analysis steps into one-liners (okay, maybe two, I'm not perfect).\n\n## Objective\nThis package serves as a complement to [Andrews, J. et al., eBioMedicine 2021](https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(21)00352-2/fulltext) and as a record of how the data was analyzed.\n\n## What It Can Do\nUltimately, this package tries to make generic RNA-seq and ChIP-seq analyses as high-level and straightforward as possible. \nIt does so by requiring only the path to a samplesheet containing sample metadata and file locations and the metadata variable of interest. \nIt will then perform RNA or ChIP-seq analyses with `DESeq2` or `DiffBind`, respectively, for all possible comparisons for the variable of interest and save the results for each analysis to disk.\n\nYou can feed it multiple p-value/FDR/fold change thresholds, and it will generate fairly nice plots for differentially expressed genes or differentially bound regions including PCA/MA plots, heatmaps, volcano plots, GO/pathway enrichment analyses, boxplots, etc., saving all of them as PDFs.\n\n## Installation\n\n```r\nrequire(\"devtools\")\ndevtools::install_github(\"j-andrews7/OneLinerOmics\")\n```\n\n## Usage\n\nPlease see the [docs](https://j-andrews7.github.io/OneLinerOmics) for a full reference and vignettes with examples (including steps like gene count quantification, peak calling, etc). \n90% of the functionality can be viewed with `?RunDESeq2` and `?RunDiffBind` after installation.\nThe [salmon](https://combine-lab.github.io/salmon/getting_started/), [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html), and [DiffBind](https://bioconductor.org/packages/release/bioc/html/DiffBind.html) manuals and vignettes may also be helpful for understanding what's going on under the hood and interpreting the output.\n\n## Issues\n\nPlease direct all complaints to [management](https://github.com/j-andrews7/OneLinerOmics/issues). \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fj-andrews7%2Fonelineromics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fj-andrews7%2Fonelineromics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fj-andrews7%2Fonelineromics/lists"}