GSR: Simulator - SymSim

Basic Package Attributes
AttributeValue
Title SymSim
Short Description SymSim simulates single cell RNA sequencing data thereby allowing users to tune the variation of gene-expression on different levels.
Long Description SymSim models the processes that give rise to data observed in single cell RNA-Seq experiments. The components of the SymSim pipeline pertain to three sources of variation in single cell RNA-Seq data: noise intrinsic to the process of transcription, extrinsic variation indicative of different cell states, and technical variation due to low sensitivity and measurement noise and bias.
Version 0.0.0.9000
Project Started 2020
Last Release 5 years, 2 months ago
Homepagehttps://github.com/YosefLab/SymSim
Citations Zhang X, Xu C, Yosef N, Simulating multiple faceted variability in single cell RNA sequencing., Nat Commun, June 13, 2019 [ Abstract, cited in PMC ]
GSR CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluatedJune 23, 2022 (1031 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 Data
Variations
Simulation Method
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
InterfaceCommand-line,
Development
Tested Platforms
LanguageR,
LicenseOther,
GSR CertificationAccessibility, Documentation, Application, Support,

Number of Primary Citations: 1

Number of Non-Primary Citations: 2

The following 2 publications are selected examples of applications that used SymSim.

2023

Boyeau P, Regier J, Gayoso A, Jordan MI, Lopez R, Yosef N, An empirical Bayes method for differential expression analysis of single cells with deep generative models., Proc Natl Acad Sci U S A, May 23, 2023 [Abstract]

2022

Buen Abad Najar CF, Burra P, Yosef N, Lareau LF, Identifying cell state-associated alternative splicing events and their coregulation., Genome Res, July 20, 2022 [Abstract]


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