SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data
Gene expression data provide an abundant resource for inferring connections in gene regulatory networks. While methodologies developed for this task have shown success, a challenge remains in comparing the performance among methods. Gold-standard datasets are scarce and limited in use. And while too...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Foundation for Open Access Statistics
2021-07-01
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| Series: | Journal of Statistical Software |
| Subjects: | |
| Online Access: | https://www.jstatsoft.org/index.php/jss/article/view/3846 |
| _version_ | 1827935794434670592 |
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| author | Tyler Grimes Somnath Datta |
| author_facet | Tyler Grimes Somnath Datta |
| author_sort | Tyler Grimes |
| collection | DOAJ |
| description | Gene expression data provide an abundant resource for inferring connections in gene regulatory networks. While methodologies developed for this task have shown success, a challenge remains in comparing the performance among methods. Gold-standard datasets are scarce and limited in use. And while tools for simulating expression data are available, they are not designed to resemble the data obtained from RNA-seq experiments. SeqNet is an R package that provides tools for generating a rich variety of gene network structures and simulating RNA-seq data from them. This produces in silico RNA-seq data for benchmarking and assessing gene network inference methods. The package is available from the Comprehensive R Archive Network at https://CRAN.R-project.org/package= SeqNet and on GitHub at https://github.com/tgrimes/SeqNet. |
| first_indexed | 2024-03-13T07:59:57Z |
| format | Article |
| id | doaj.art-487cb3f307904ce1bcdd5796cc80d6c8 |
| institution | Directory Open Access Journal |
| issn | 1548-7660 |
| language | English |
| last_indexed | 2024-03-13T07:59:57Z |
| publishDate | 2021-07-01 |
| publisher | Foundation for Open Access Statistics |
| record_format | Article |
| series | Journal of Statistical Software |
| spelling | doaj.art-487cb3f307904ce1bcdd5796cc80d6c82023-06-01T18:41:06ZengFoundation for Open Access StatisticsJournal of Statistical Software1548-76602021-07-0198110.18637/jss.v098.i123660SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq DataTyler GrimesSomnath DattaGene expression data provide an abundant resource for inferring connections in gene regulatory networks. While methodologies developed for this task have shown success, a challenge remains in comparing the performance among methods. Gold-standard datasets are scarce and limited in use. And while tools for simulating expression data are available, they are not designed to resemble the data obtained from RNA-seq experiments. SeqNet is an R package that provides tools for generating a rich variety of gene network structures and simulating RNA-seq data from them. This produces in silico RNA-seq data for benchmarking and assessing gene network inference methods. The package is available from the Comprehensive R Archive Network at https://CRAN.R-project.org/package= SeqNet and on GitHub at https://github.com/tgrimes/SeqNet.https://www.jstatsoft.org/index.php/jss/article/view/3846gene regulatory networksco-expression methodsdifferential network analysisGaussian graphical model |
| spellingShingle | Tyler Grimes Somnath Datta SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data Journal of Statistical Software gene regulatory networks co-expression methods differential network analysis Gaussian graphical model |
| title | SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data |
| title_full | SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data |
| title_fullStr | SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data |
| title_full_unstemmed | SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data |
| title_short | SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data |
| title_sort | seqnet an r package for generating gene gene networks and simulating rna seq data |
| topic | gene regulatory networks co-expression methods differential network analysis Gaussian graphical model |
| url | https://www.jstatsoft.org/index.php/jss/article/view/3846 |
| work_keys_str_mv | AT tylergrimes seqnetanrpackageforgeneratinggenegenenetworksandsimulatingrnaseqdata AT somnathdatta seqnetanrpackageforgeneratinggenegenenetworksandsimulatingrnaseqdata |