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Negative binomial model
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This cross-sectional cohort study assessed the inequalities in oesophageal carcinoma risk by age, sex and nativity in Kuwait: 1980–2019. Methods Using oesophageal cancer incidence data from the Kuwait National Cancer Registry, relevant Kuwaiti population data and World Standard Population as a reference, age-standardized incidence rates (ASIR) (per 100,000 person-years) overall and by subcohorts were computed.
5p
vischultz
20-10-2023
1
1
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Single-cell RNA-seq (scRNA-seq) data exhibits significant cell-to-cell variation due to technical factors, including the number of molecules detected in each cell, which can confound biological heterogeneity with technical effects. To address this, we present a modeling framework for the normalization and variance stabilization of molecular count data from scRNA-seq experiments.
15p
vielonmusk
30-01-2022
8
0
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High-throughput CRISPR screens have shown great promise in functional genomics. We present MAGeCK-VISPR, a comprehensive quality control (QC), analysis, and visualization workflow for CRISPR screens. MAGeCK-VISPR defines a set of QC measures to assess the quality of an experiment, and includes a maximum-likelihood algorithm to call essential genes simultaneously under multiple conditions.
13p
viaristotle
29-01-2022
12
0
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Sample size calculation is an important issue in the experimental design of biomedical research. For RNA-seq experiments, the sample size calculation method based on the Poisson model has been proposed; however, when there are biological replicates, RNA-seq data could exhibit variation significantly greater than the mean (i.e. over-dispersion).
7p
viwyoming2711
16-12-2020
10
0
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Microbiome/metagenomic data have specific characteristics, including varying total sequence reads, over-dispersion, and zero-inflation, which require tailored analytic tools.
19p
vikentucky2711
24-11-2020
17
2
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Accurate identification of differentially expressed (DE) genes in time course RNA-Seq data is crucial for understanding the dynamics of transcriptional regulatory network. However, most of the available methods treat gene expressions at different time points as replicates and test the significance of the mean expression difference between treatments or conditions irrespective of time.
13p
vioklahoma2711
19-11-2020
21
2
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Heritability of a phenotypic or molecular trait measures the proportion of variance that is attributable to genotypic variance. It is an important concept in breeding and genetics. Few methods are available for calculating heritability for traits derived from high-throughput sequencing.
16p
vioklahoma2711
19-11-2020
8
1
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Next generation sequencing provides a count of RNA molecules in the form of short reads, yielding discrete, often highly non-normally distributed gene expression measurements. Although Negative Binomial (NB) regression has been generally accepted in the analysis of RNA sequencing (RNA-Seq) data, its appropriateness has not been exhaustively evaluated.
13p
vioklahoma2711
19-11-2020
12
1
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Recent advances in next-generation sequencing (NGS) technology enable researchers to collect a large volume of metagenomic sequencing data. These data provide valuable resources for investigating interactions between the microbiome and host environmental/clinical factors.
10p
vioklahoma2711
19-11-2020
13
0
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As a newly emerged research area, RNA epigenetics has drawn increasing attention recently for the participation of RNA methylation and other modifications in a number of crucial biological processes.
12p
viflorida2711
30-10-2020
15
3
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Inference of gene regulatory network structures from RNA-Seq data is challenging due to the nature of the data, as measurements take the form of counts of reads mapped to a given gene. Here we present a model for RNA-Seq time series data that applies a negative binomial distribution for the observations, and uses sparse regression with a horseshoe prior to learn a dynamic Bayesian network of interactions between genes.
12p
viconnecticut2711
28-10-2020
19
0
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Unsupervised clustering represents one of the most widely applied methods in analysis of highthroughput ‘omics data. A variety of unsupervised model-based or parametric clustering methods and nonparametric clustering methods have been proposed for RNA-seq count data, most of which perform well for large samples, e.g. N ≥ 500.
10p
vicoachella2711
27-10-2020
11
0
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Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) is a popular sequencing method for studying RNA modifications and, in particular, for N6-methyladenosine (m6A), the most abundant RNA methylation modification found in various species.
12p
vicolorado2711
22-10-2020
6
0
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High-throughput sequencing experiments followed by differential expression analysis is a widely used approach for detecting genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and covariates of interest.
15p
vicolorado2711
22-10-2020
15
0
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Power analysis becomes an inevitable step in experimental design of current biomedical research. Complex designs allowing diverse correlation structures are commonly used in RNA-Seq experiments. However, the field currently lacks statistical methods to calculate sample size and estimate power for RNA-Seq differential expression studies using such designs.
12p
vicolorado2711
22-10-2020
27
0
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: Interpreting clinical guideline adherence and the appropriateness of medication regimens requires consideration of individual patient and caregiver factors. Factors leading to initiation of a medication may differ from those determining continued use.
10p
vienzym2711
30-03-2020
10
1
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In this article, our primary interest is to compare and discuss about the criteria for selecting model and its applications. The authors provide approaches and procedures of these methods and apply to the tra c violation data where we look for the most appropriate model among Poisson regression.
11p
vioishi2711
01-07-2019
20
0
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In this research, the dead trees were defined as the standing trees that died between the two occasions at which measurements were taken. The data on 300 subplots from 12 permanent sample plots were collected. The response variable was the number of dead trees per subplot.
11p
nutifooddau
18-01-2019
25
1
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Regional determinants of FDI location in Vietnam. This paper examines empirically determinants of foreign direct investment (FDI) location in Vietnam. Based on a panel dataset of 63 provinces and cities in Vietnam from 2008 to 2012, linear regression models for panel data (fixed-effects and random-effects) and negative binomial models are applied in analysis.
19p
tranminhluanluan
28-05-2018
50
6
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Lecture "Advanced Econometrics (Part II) - Chapter 6: Models for count data" presentation of content: Poisson regression model, goodness of fit, overdispersion, negative binomial regression model, too many zeros data.
7p
nghe123
06-05-2016
77
3
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