scbursts: An R package for analysis and sorting of single-channel bursts
Analysis of single-channel activity provides unparalleled insight into ion channel structure, function, and mechanism. An essential step in the analysis pipeline is the assignment and sorting of bursts of activity that can be attributed to a single ion channel. Here we present scbursts, an R package...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2019-07-01
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| Series: | SoftwareX |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352711019300810 |
| _version_ | 1811325635477372928 |
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| author | Blair R. Drummond Christian J.G. Tessier Mathieu F. Dextraze Corrie J.B. daCosta |
| author_facet | Blair R. Drummond Christian J.G. Tessier Mathieu F. Dextraze Corrie J.B. daCosta |
| author_sort | Blair R. Drummond |
| collection | DOAJ |
| description | Analysis of single-channel activity provides unparalleled insight into ion channel structure, function, and mechanism. An essential step in the analysis pipeline is the assignment and sorting of bursts of activity that can be attributed to a single ion channel. Here we present scbursts, an R package for the analysis and sorting of single-channel bursts. Using scbursts, idealized data from a variety of single-channel analysis software packages can be read directly into R, and parsed into bursts according to a user-defined critical closed duration. Bursts can be analyzed and sorted based on a variety of parameters, including burst open probability, and the number of openings per burst. Sorted bursts can then be exported in a standard format for downstream kinetic fitting. We provide examples illustrating the implementation and utility of scbursts, as well as how scbursts brings the statistical prowess and versatility of R to single-channel analysis. Keywords: Single-molecule analysis, single-channel analysis, bursts, ion channel, kinetic fitting |
| first_indexed | 2024-04-13T14:36:38Z |
| format | Article |
| id | doaj.art-0bd6265d90794ca39d3e51e41aa42d47 |
| institution | Directory Open Access Journal |
| issn | 2352-7110 |
| language | English |
| last_indexed | 2024-04-13T14:36:38Z |
| publishDate | 2019-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | SoftwareX |
| spelling | doaj.art-0bd6265d90794ca39d3e51e41aa42d472022-12-22T02:43:01ZengElsevierSoftwareX2352-71102019-07-0110scbursts: An R package for analysis and sorting of single-channel burstsBlair R. Drummond0Christian J.G. Tessier1Mathieu F. Dextraze2Corrie J.B. daCosta3Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, CanadaCentre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, CanadaCentre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, CanadaCorresponding author.; Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, CanadaAnalysis of single-channel activity provides unparalleled insight into ion channel structure, function, and mechanism. An essential step in the analysis pipeline is the assignment and sorting of bursts of activity that can be attributed to a single ion channel. Here we present scbursts, an R package for the analysis and sorting of single-channel bursts. Using scbursts, idealized data from a variety of single-channel analysis software packages can be read directly into R, and parsed into bursts according to a user-defined critical closed duration. Bursts can be analyzed and sorted based on a variety of parameters, including burst open probability, and the number of openings per burst. Sorted bursts can then be exported in a standard format for downstream kinetic fitting. We provide examples illustrating the implementation and utility of scbursts, as well as how scbursts brings the statistical prowess and versatility of R to single-channel analysis. Keywords: Single-molecule analysis, single-channel analysis, bursts, ion channel, kinetic fittinghttp://www.sciencedirect.com/science/article/pii/S2352711019300810 |
| spellingShingle | Blair R. Drummond Christian J.G. Tessier Mathieu F. Dextraze Corrie J.B. daCosta scbursts: An R package for analysis and sorting of single-channel bursts SoftwareX |
| title | scbursts: An R package for analysis and sorting of single-channel bursts |
| title_full | scbursts: An R package for analysis and sorting of single-channel bursts |
| title_fullStr | scbursts: An R package for analysis and sorting of single-channel bursts |
| title_full_unstemmed | scbursts: An R package for analysis and sorting of single-channel bursts |
| title_short | scbursts: An R package for analysis and sorting of single-channel bursts |
| title_sort | scbursts an r package for analysis and sorting of single channel bursts |
| url | http://www.sciencedirect.com/science/article/pii/S2352711019300810 |
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