GSR: Simulator - LSH-GAN

Basic Package Attributes
AttributeValue
Title LSH-GAN
Short Description LSH-GAN enables in-silico generation of cells for small sample high dimensional scRNA-seq data
Long Description A fundamental problem of downstream analysis of scRNA-seq data is the unavailability of enough cell samples compare to the feature size. This is mostly due to the budgetary constraint of single cell experiments or simply because of the small number of available patient samples. Here, we present an improved version of generative adversarial network (GAN) called LSH-GAN to address this issue by producing new realistic cell samples. We update the training procedure of the generator of GAN using locality sensitive hashing which speeds up the sample generation, thus maintains the feasibility of applying the standard procedures of downstream analysis. LSH-GAN outperforms the benchmarks for realistic generation of quality cell samples. Experimental results show that generated samples of LSH-GAN improves the performance of the downstream analysis such as feature (gene) selection and cell clustering. Overall, LSH-GAN therefore addressed the key challenges of small sample scRNA-seq data analysis.
Keywords single-cell RNA sequencing, scRNA-seq, HDSS data, Machine learning, Computational models
Version 1.0.0
Project Started 2021
Last Release 3 years, 6 months ago
Homepagehttps://github.com/Snehalikalall/LSH-GAN
Citations Lall S, Ray S, Bandyopadhyay S, LSH-GAN enables in-silico generation of cells for small sample high dimensional scRNA-seq data., Commun Biol, June 10, 2022 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluatedDec. 9, 2022 (862 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, Single-Cell Sequencing,
VariationsSingle Nucleotide Variation,
Simulation MethodMachine Learning,
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, Python,
License
GSR CertificationSupport,

Number of Primary Citations: 1

Number of Non-Primary Citations: 0

No example publication using LSH-GAN has been provided.

Please propose new citations if you are aware of publications that use this software.


Propose changes to this simulator