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GSR: Simulator - CAMPAREE
| Attribute | Value |
|---|---|
| Title | CAMPAREE |
| Short Description | a robust and configurable RNA expression simulator |
| Long Description | CAMPAREE is a RNA expression simulator that is primed using real data to give realistic output. CAMPAREE needs as input a reference genome with transcript annotations as well as fastq files of samples of the species to base the output on. For each sample, CAMPAREE outputs a simulated set of RNA transcripts mimicking expression levels with in the fastq files and accounting for isoform-level expression and allele-specific expression. It also outputs simulated diploid genomes and their corresponding annotations with phased SNP and indel calls in the transcriptome from fastq reads. Additionally the simulation outputs the underlying distributions used for expressing the transcripts. |
| Version | 0.3.0 |
| Last Release | 4 years ago |
| Homepage | https://github.com/itmat/CAMPAREE |
| Citations | Lahens NF, Brooks TG, Sarantopoulou D, Nayak S, Lawrence C, Mrčela A, Srinivasan A, Schug J, Hogenesch JB, Barash Y, et al., CAMPAREE: a robust and configurable RNA expression simulator., BMC Genomics, Sept. 25, 2021 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | March 8, 2022 (1262 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, Gene Expression, |
| Variations | |
| Simulation Method | |
| Input | |
| Data Type | Reference genome, |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | Other, |
| File Format | Fasta or Fastq, |
| 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 | Windows, Mac OS X, Linux and Unix, |
| Language | Python, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using CAMPAREE has been provided.
Please propose new citations if you are aware of publications that use this software.