GSR: Simulator - Polyester

Basic Package Attributes
AttributeValue
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 1 year, 8 months ago
Homepagehttp://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, 09-01-2015 [ Abstract, cited in PMC ]
GSR CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluated07-08-2021 (71 days ago)
Author verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataRNA,
Variations
Simulation MethodOther,
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
LanguageR,
LicenseOther,
GSR CertificationAccessibility, Documentation, Application, Support,

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, 04-29-2021 [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, 04-29-2021 [Abstract]

Ma C, Zheng H, Kingsford C, Exact transcript quantification over splice graphs., Algorithms Mol Biol, 05-10-2021 [Abstract]

Ma C, Zheng H, Kingsford C, Exact transcript quantification over splice graphs., Algorithms Mol Biol, 05-10-2021 [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, 05-14-2021 [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, 05-14-2021 [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, 06-26-2021 [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, 06-26-2021 [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, 06-23-2021 [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, 06-23-2021 [Abstract]


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