SymSim simulates single cell RNA sequencing data thereby allowing users to tune the variation of gene-expression on different levels. Long Description (required)
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. https://github.com/YosefLab/SymSim zhangxiuwei03@gmail.com
Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.
Every sub-attribute is selected Not all sub-attributes are selectedFill Clear Expand Collapse Reset
Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s).
Can't Find the Attribute You Are Looking For? If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab .
Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 31197158 ],
Zhang X, Xu C, Yosef N ,
Simulating multiple faceted variability in single cell RNA sequencing. ,
Nat Commun ,
06-13-2019 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=31197158, Primary Citation
[Pubmed ID: 35858747 ],
Buen Abad Najar CF, Burra P, Yosef N, Lareau LF ,
Identifying cell state-associated alternative splicing events and their coregulation. ,
Genome Res ,
07-20-2022 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=35858747, , Application
[Pubmed ID: 37192164 ],
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 ,
05-23-2023 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=37192164, , Application