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Add support for CITATION.cff (#39)
GitHub [supports](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files) having a `CITATION.cff` file to add a citation option to your repository, added a `CITATION.cff` based off of <https://doi.org/10.1111/tpj.14468>.
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.gitignore

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renv/python
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renv/.gitignore
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# Python virtual environment
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venv/

CITATION.cff

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cff-version: 1.2.0
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title: eFP-Seq Browser
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message: >-
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An 'eFP-Seq Browser' for visualizing and exploring RNA
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sequencing data
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type: software
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authors:
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- given-names: Alexander
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family-names: Sullivan
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email: alexjsully.connect@outlook.com
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orcid: "https://orcid.org/0000-0002-4463-4473"
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- given-names: Priyank K.
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family-names: Purohit
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- given-names: Nowlan H.
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family-names: Freese
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- given-names: Asher
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family-names: Pasha
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orcid: "https://orcid.org/0000-0002-9315-0520"
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- given-names: Eddi
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family-names: Esteban
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orcid: "https://orcid.org/0000-0001-9016-9202"
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- given-names: Jamie
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family-names: Waese
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- given-names: Alison
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family-names: Wu
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- given-names: Michelle
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family-names: Chen
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- given-names: Chih Y.
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family-names: Chin
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- given-names: Richard
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family-names: Song
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- given-names: Sneha R.
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family-names: Watharkar
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- given-names: Agnes P.
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family-names: Chan
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- given-names: Vivek
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family-names: Krishnakumar
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- given-names: Matthew W.
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family-names: Vaughn
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- given-names: Chris
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family-names: Town
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- given-names: Ann E.
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family-names: Loraine
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affiliation: University of North Carolina
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email: ann.loraine@uncc.edu
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- given-names: Nicholas J.
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family-names: Provart
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orcid: "https://orcid.org/0000-0001-5551-7232"
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email: nicholas.provart@utoronto.ca
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affiliation: University of Toronto
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identifiers:
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- type: doi
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value: 10.1111/tpj.14468
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repository-code: "https://github.com/BioAnalyticResource/eFP-Seq_Browser"
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url: "https://bar.utoronto.ca/eFP-Seq_Browser/"
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abstract: >-
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Improvements in next-generation sequencing technologies
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have resulted in dramatically reduced sequencing costs.
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This has led to an explosion of '-seq'-based methods, of
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which RNA sequencing (RNA-seq) for generating
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transcriptomic data is the most popular. By analysing
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global patterns of gene expression in organs/tissues/cells
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of interest or in response to chemical or environmental
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perturbations, researchers can better understand an
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organism's biology. Tools designed to work with large
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RNA-seq data sets enable analyses and visualizations to
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help generate hypotheses about a gene's function. We
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present here a user-friendly RNA-seq data exploration
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tool, called the 'eFP-Seq Browser', that shows the read
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map coverage of a gene of interest in each of the samples
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along with 'electronic fluorescent pictographic' (eFP)
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images that serve as visual representations of expression
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levels. The tool also summarizes the details of each
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RNA-seq experiment, providing links to archival databases
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and publications. It automatically computes the reads per
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kilobase per million reads mapped expression-level
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summaries and point biserial correlation scores to sort
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the samples based on a gene's expression level or by how
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dissimilar the read map profile is from a gene splice
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variant, to quickly identify samples with the strongest
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expression level or where alternative splicing might be
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occurring. Links to the Integrated Genome Browser desktop
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visualization tool allow researchers to visualize and
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explore the details of RNA-seq alignments summarized in
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eFP-Seq Browser as coverage graphs. We present four cases
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of use of the eFP-Seq Browser for ABI3, SR34, SR45a and
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U2AF65B, where we examine expression levels and identify
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alternative splicing. The URL for the browser is
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https://bar.utoronto.ca/eFP-Seq_Browser/.
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keywords:
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- bioinformatics
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- computational biology
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- rna-seq
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- data visualization
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- arabidopsis thaliana
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- rna-seq mapping
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- alternative splicing
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- web application
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license: GPL-2.0
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commit: a5b952bf2df11e9c8538b372f2ee0d3c23d1fa90
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version: 1.3.15
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date-released: "2024-01-15"

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