Biomaterial Database

SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data. 2020

Alemu Takele Assefa, and Jo Vandesompele, and Olivier Thas

Data Analysis and Mathematical Modeling.

SPsimSeq is a semi-parametric simulation method to generate bulk and single-cell RNA-sequencing data. It is designed to simulate gene expression data with maximal retention of the characteristics of real data. It is reasonably flexible to accommodate a wide range of experimental scenarios, including different sample sizes, biological signals (differential expression) and confounding batch effects. The R package and associated documentation is available from https://github.com/CenterForStatistics-UGent/SPsimSeq. Supplementary data are available at Bioinformatics online.

UI	MeSH Term	Description	Entries
D000073359	Exome Sequencing	Techniques used to determine the sequences of EXONS of an organism or individual.	Complete Exome Sequencing,Complete Transcriptome Sequencing,Whole Exome Sequencing,Whole Transcriptome Sequencing,Complete Exome Sequencings,Exome Sequencing, Complete,Exome Sequencing, Whole,Exome Sequencings, Complete,Sequencing, Complete Exome,Sequencing, Complete Transcriptome,Sequencing, Exome,Sequencing, Whole Exome,Sequencing, Whole Transcriptome,Transcriptome Sequencing, Complete,Transcriptome Sequencing, Whole,Transcriptome Sequencings, Complete
D001483	Base Sequence	The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.	DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D012313	RNA	A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)	RNA, Non-Polyadenylated,Ribonucleic Acid,Gene Products, RNA,Non-Polyadenylated RNA,Acid, Ribonucleic,Non Polyadenylated RNA,RNA Gene Products,RNA, Non Polyadenylated
D012984	Software	Sequential operating programs and data which instruct the functioning of a digital computer.	Computer Programs,Computer Software,Open Source Software,Software Engineering,Software Tools,Computer Applications Software,Computer Programs and Programming,Computer Software Applications,Application, Computer Software,Applications Software, Computer,Applications Softwares, Computer,Applications, Computer Software,Computer Applications Softwares,Computer Program,Computer Software Application,Engineering, Software,Open Source Softwares,Program, Computer,Programs, Computer,Software Application, Computer,Software Applications, Computer,Software Tool,Software, Computer,Software, Computer Applications,Software, Open Source,Softwares, Computer Applications,Softwares, Open Source,Source Software, Open,Source Softwares, Open,Tool, Software,Tools, Software
D017423	Sequence Analysis, RNA	A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.	RNA Sequence Analysis,Sequence Determination, RNA,Analysis, RNA Sequence,Determination, RNA Sequence,Determinations, RNA Sequence,RNA Sequence Determination,RNA Sequence Determinations,RNA Sequencing,Sequence Determinations, RNA,Analyses, RNA Sequence,RNA Sequence Analyses,Sequence Analyses, RNA,Sequencing, RNA