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| 1 | +cff-version: 1.2.0 |
| 2 | +title: eFP-Seq Browser |
| 3 | +message: >- |
| 4 | + An 'eFP-Seq Browser' for visualizing and exploring RNA |
| 5 | + sequencing data |
| 6 | +type: software |
| 7 | +authors: |
| 8 | + - given-names: Alexander |
| 9 | + family-names: Sullivan |
| 10 | + email: alexjsully.connect@outlook.com |
| 11 | + orcid: "https://orcid.org/0000-0002-4463-4473" |
| 12 | + - given-names: Priyank K. |
| 13 | + family-names: Purohit |
| 14 | + - given-names: Nowlan H. |
| 15 | + family-names: Freese |
| 16 | + - given-names: Asher |
| 17 | + family-names: Pasha |
| 18 | + orcid: "https://orcid.org/0000-0002-9315-0520" |
| 19 | + - given-names: Eddi |
| 20 | + family-names: Esteban |
| 21 | + orcid: "https://orcid.org/0000-0001-9016-9202" |
| 22 | + - given-names: Jamie |
| 23 | + family-names: Waese |
| 24 | + - given-names: Alison |
| 25 | + family-names: Wu |
| 26 | + - given-names: Michelle |
| 27 | + family-names: Chen |
| 28 | + - given-names: Chih Y. |
| 29 | + family-names: Chin |
| 30 | + - given-names: Richard |
| 31 | + family-names: Song |
| 32 | + - given-names: Sneha R. |
| 33 | + family-names: Watharkar |
| 34 | + - given-names: Agnes P. |
| 35 | + family-names: Chan |
| 36 | + - given-names: Vivek |
| 37 | + family-names: Krishnakumar |
| 38 | + - given-names: Matthew W. |
| 39 | + family-names: Vaughn |
| 40 | + - given-names: Chris |
| 41 | + family-names: Town |
| 42 | + - given-names: Ann E. |
| 43 | + family-names: Loraine |
| 44 | + affiliation: University of North Carolina |
| 45 | + email: ann.loraine@uncc.edu |
| 46 | + - given-names: Nicholas J. |
| 47 | + family-names: Provart |
| 48 | + orcid: "https://orcid.org/0000-0001-5551-7232" |
| 49 | + email: nicholas.provart@utoronto.ca |
| 50 | + affiliation: University of Toronto |
| 51 | +identifiers: |
| 52 | + - type: doi |
| 53 | + value: 10.1111/tpj.14468 |
| 54 | +repository-code: "https://github.com/BioAnalyticResource/eFP-Seq_Browser" |
| 55 | +url: "https://bar.utoronto.ca/eFP-Seq_Browser/" |
| 56 | +abstract: >- |
| 57 | + Improvements in next-generation sequencing technologies |
| 58 | + have resulted in dramatically reduced sequencing costs. |
| 59 | + This has led to an explosion of '-seq'-based methods, of |
| 60 | + which RNA sequencing (RNA-seq) for generating |
| 61 | + transcriptomic data is the most popular. By analysing |
| 62 | + global patterns of gene expression in organs/tissues/cells |
| 63 | + of interest or in response to chemical or environmental |
| 64 | + perturbations, researchers can better understand an |
| 65 | + organism's biology. Tools designed to work with large |
| 66 | + RNA-seq data sets enable analyses and visualizations to |
| 67 | + help generate hypotheses about a gene's function. We |
| 68 | + present here a user-friendly RNA-seq data exploration |
| 69 | + tool, called the 'eFP-Seq Browser', that shows the read |
| 70 | + map coverage of a gene of interest in each of the samples |
| 71 | + along with 'electronic fluorescent pictographic' (eFP) |
| 72 | + images that serve as visual representations of expression |
| 73 | + levels. The tool also summarizes the details of each |
| 74 | + RNA-seq experiment, providing links to archival databases |
| 75 | + and publications. It automatically computes the reads per |
| 76 | + kilobase per million reads mapped expression-level |
| 77 | + summaries and point biserial correlation scores to sort |
| 78 | + the samples based on a gene's expression level or by how |
| 79 | + dissimilar the read map profile is from a gene splice |
| 80 | + variant, to quickly identify samples with the strongest |
| 81 | + expression level or where alternative splicing might be |
| 82 | + occurring. Links to the Integrated Genome Browser desktop |
| 83 | + visualization tool allow researchers to visualize and |
| 84 | + explore the details of RNA-seq alignments summarized in |
| 85 | + eFP-Seq Browser as coverage graphs. We present four cases |
| 86 | + of use of the eFP-Seq Browser for ABI3, SR34, SR45a and |
| 87 | + U2AF65B, where we examine expression levels and identify |
| 88 | + alternative splicing. The URL for the browser is |
| 89 | + https://bar.utoronto.ca/eFP-Seq_Browser/. |
| 90 | +keywords: |
| 91 | + - bioinformatics |
| 92 | + - computational biology |
| 93 | + - rna-seq |
| 94 | + - data visualization |
| 95 | + - arabidopsis thaliana |
| 96 | + - rna-seq mapping |
| 97 | + - alternative splicing |
| 98 | + - web application |
| 99 | +license: GPL-2.0 |
| 100 | +commit: a5b952bf2df11e9c8538b372f2ee0d3c23d1fa90 |
| 101 | +version: 1.3.15 |
| 102 | +date-released: "2024-01-15" |
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