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GSR: Simulator - Polyester
| Attribute | Value |
|---|---|
| Title | Polyester |
| Short Description | simulating RNA-seq datasets with differential transcript expression |
| Long Description | simulate RNA-seq reads from differential expression experiments with replicates. The reads can then be aligned and used to perform comparisons of methods for differential expression. |
| Version | 1.26.0 |
| Last Release | 5 years, 8 months ago |
| Homepage | http://bioconductor.org/packages/release/bioc/html/polyester.html |
| Citations | Frazee AC, Jaffe AE, Langmead B, Leek JT, Polyester: simulating RNA-seq datasets with differential transcript expression., Bioinformatics, Sept. 1, 2015 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | July 8, 2021 (1506 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | RNA, |
| Variations | |
| Simulation Method | Other, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | |
| File Format | |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | |
| Development | |
| Tested Platforms | |
| Language | R, |
| License | Other, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 10
The following 10 publications are selected examples of applications that used Polyester.
2021
Chung M, Bruno VM, Rasko DA, Cuomo CA, Muñoz JF, Livny J, Shetty AC, Mahurkar A, Dunning Hotopp JC, Best practices on the differential expression analysis of multi-species RNA-seq., Genome Biol, April 29, 2021 [Abstract]
Chung M, Bruno VM, Rasko DA, Cuomo CA, Muñoz JF, Livny J, Shetty AC, Mahurkar A, Dunning Hotopp JC, Best practices on the differential expression analysis of multi-species RNA-seq., Genome Biol, April 29, 2021 [Abstract]
Ma C, Zheng H, Kingsford C, Exact transcript quantification over splice graphs., Algorithms Mol Biol, May 10, 2021 [Abstract]
Ma C, Zheng H, Kingsford C, Exact transcript quantification over splice graphs., Algorithms Mol Biol, May 10, 2021 [Abstract]
Dent CI, Singh S, Mukherjee S, Mishra S, Sarwade RD, Shamaya N, Loo KP, Harrison P, Sureshkumar S, Powell D, et al., Quantifying splice-site usage: a simple yet powerful approach to analyze splicing., NAR Genom Bioinform, May 14, 2021 [Abstract]
Dent CI, Singh S, Mukherjee S, Mishra S, Sarwade RD, Shamaya N, Loo KP, Harrison P, Sureshkumar S, Powell D, et al., Quantifying splice-site usage: a simple yet powerful approach to analyze splicing., NAR Genom Bioinform, May 14, 2021 [Abstract]
Goering R, Engel KL, Gillen AE, Fong N, Bentley DL, Taliaferro JM, LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival., BMC Genomics, June 26, 2021 [Abstract]
Goering R, Engel KL, Gillen AE, Fong N, Bentley DL, Taliaferro JM, LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival., BMC Genomics, June 26, 2021 [Abstract]
Riquier S, Bessiere C, Guibert B, Bouge AL, Boureux A, Ruffle F, Audoux J, Gilbert N, Xue H, Gautheret D, et al., Kmerator Suite: design of specific <i>k</i>-mer signatures and automatic metadata discovery in large RNA-seq datasets., NAR Genom Bioinform, June 23, 2021 [Abstract]
Riquier S, Bessiere C, Guibert B, Bouge AL, Boureux A, Ruffle F, Audoux J, Gilbert N, Xue H, Gautheret D, et al., Kmerator Suite: design of specific <i>k</i>-mer signatures and automatic metadata discovery in large RNA-seq datasets., NAR Genom Bioinform, June 23, 2021 [Abstract]