siMacro: A Fast and Easy Data Processing Tool for Cell-Based Genomewide siRNA Screens
Growing numbers of studies employ cell line-based systematic short interfering RNA (siRNA) screens to study gene functions and to identify drug targets. As multiple sources of variations that are unique to siRNA screens exist, there is a growing demand for a computational tool that generates normali...
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| Format: | Article |
| Language: | English |
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BioMed Central
2013-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-11-55.pdf |
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| author | Nitin Kumar Singh Bo Yeun Seo Mathukumalli Vidyasagar Michael A. White Hyun Seok Kim |
| author_facet | Nitin Kumar Singh Bo Yeun Seo Mathukumalli Vidyasagar Michael A. White Hyun Seok Kim |
| author_sort | Nitin Kumar Singh |
| collection | DOAJ |
| description | Growing numbers of studies employ cell line-based systematic short interfering RNA (siRNA) screens to study gene functions and to identify drug targets. As multiple sources of variations that are unique to siRNA screens exist, there is a growing demand for a computational tool that generates normalized values and standardized scores. However, only a few tools have been available so far with limited usability. Here, we present siMacro, a fast and easy-to-use Microsoft Office Excel-based tool with a graphic user interface, designed to process single-condition or two-condition synthetic screen datasets. siMacro normalizes position and batch effects, censors outlier samples, and calculates Z-scores and robust Z-scores, with a spreadsheet output of >120,000 samples in under 1 minute. |
| format | Article |
| id | doaj-art-e1c93eef5eff4aa1b8c044523fb35628 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2013-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-e1c93eef5eff4aa1b8c044523fb356282025-02-02T19:15:32ZengBioMed CentralGenomics & Informatics1598-866X2234-07422013-03-01111555710.5808/GI.2013.11.1.5578siMacro: A Fast and Easy Data Processing Tool for Cell-Based Genomewide siRNA ScreensNitin Kumar Singh0Bo Yeun Seo1Mathukumalli Vidyasagar2Michael A. White3Hyun Seok Kim4Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA.Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA.Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.Growing numbers of studies employ cell line-based systematic short interfering RNA (siRNA) screens to study gene functions and to identify drug targets. As multiple sources of variations that are unique to siRNA screens exist, there is a growing demand for a computational tool that generates normalized values and standardized scores. However, only a few tools have been available so far with limited usability. Here, we present siMacro, a fast and easy-to-use Microsoft Office Excel-based tool with a graphic user interface, designed to process single-condition or two-condition synthetic screen datasets. siMacro normalizes position and batch effects, censors outlier samples, and calculates Z-scores and robust Z-scores, with a spreadsheet output of >120,000 samples in under 1 minute.http://genominfo.org/upload/pdf/gni-11-55.pdfhigh-throughput screening assaysRNA interference |
| spellingShingle | Nitin Kumar Singh Bo Yeun Seo Mathukumalli Vidyasagar Michael A. White Hyun Seok Kim siMacro: A Fast and Easy Data Processing Tool for Cell-Based Genomewide siRNA Screens Genomics & Informatics high-throughput screening assays RNA interference |
| title | siMacro: A Fast and Easy Data Processing Tool for Cell-Based Genomewide siRNA Screens |
| title_full | siMacro: A Fast and Easy Data Processing Tool for Cell-Based Genomewide siRNA Screens |
| title_fullStr | siMacro: A Fast and Easy Data Processing Tool for Cell-Based Genomewide siRNA Screens |
| title_full_unstemmed | siMacro: A Fast and Easy Data Processing Tool for Cell-Based Genomewide siRNA Screens |
| title_short | siMacro: A Fast and Easy Data Processing Tool for Cell-Based Genomewide siRNA Screens |
| title_sort | simacro a fast and easy data processing tool for cell based genomewide sirna screens |
| topic | high-throughput screening assays RNA interference |
| url | http://genominfo.org/upload/pdf/gni-11-55.pdf |
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