Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
نویسندگان
چکیده
منابع مشابه
Estimation of Count Data using Bivariate Negative Binomial Regression Models
Abstract Negative binomial regression model (NBR) is a popular approach for modeling overdispersed count data with covariates. Several parameterizations have been performed for NBR, and the two well-known models, negative binomial-1 regression model (NBR-1) and negative binomial-2 regression model (NBR-2), have been applied. Another parameterization of NBR is negative binomial-P regression mode...
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We have assessed the performance of seven normalization methods for single cell RNA-seq using data generated from dilution of RNA samples. Our analyses showed that methods considering spike-in External RNA Control Consortium (ERCC) RNA molecules significantly outperformed those not considering ERCCs. This work provides a guidance of selecting normalization methods to remove technical noise in s...
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The analysis of RNA-Seq data has been focused on three main categories, including gene expression, relative exon usage and transcript expression. Methods have been proposed independently for each category using a negative binomial (NB) model. However, counts following a NB distribution on one feature (e.g., exon) do not guarantee a NB distribution for the other two features (e.g., gene/transcri...
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Motivation Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) an...
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ژورنال
عنوان ژورنال: Genome Biology
سال: 2019
ISSN: 1474-760X
DOI: 10.1186/s13059-019-1874-1