simSplicing

This alternative splicing count data were created 
by simulating dorsal and ventral RNA-sequence 
count data.

datasets

We constructed 'NBBttest' for identifying genes or RNA isoforms differentially expressed between two conditions on RNA-seq count data. Package 'NBBttest' can perform data quality check, data normalization, differential analysis, annotation and graphic analysis. In differential analysis, 'NBBttest' can identify differentially expressed genes and differential RNA isoforms in alternative splicing sites and alternative polyadenylation sites, differential sgRNA, and differential CRISPR (clustered regularly interspaced short palindromic repeats) screening genes. In graphic analysis, 'NBBttest' provides two types of heatmaps to visualize differential expression at gene or isoform level using z-score and n-score and creates pathway heatmap. 'NBBttest' can plot differentially expressed exons within a specified gene. In addition, 'NBBttest' provides a tool for annotation of genes and exons. The methods used in 'NBBttest' were new statistical methods developed from Tan and others (2015) <doi:10.1371/journal.pone.0123658>. The statistical methods are robust and very powerful in identifying genes or RNA isoforms differentially expressed between two conditions in small samples.

YuanDe Tan

NBBttest

Negative Binomial Beta t-Test

simSplicing function

A data frame with 5000 observations on the following 
9 variables.<dl class="dl-horizontal">
 <dt><code>Isoform</code></dt><dd>a factor with levels</dd>
 <dt><code>geneid</code></dt><dd>a factor with levels</dd>
 <dt><code>label</code></dt><dd>a numeric vector</dd>
 <dt><code>D1</code></dt><dd>a numeric vector</dd>
 <dt><code>D2</code></dt><dd>a numeric vector</dd>
 <dt><code>D3</code></dt><dd>a numeric vector</dd>
 <dt><code>V1</code></dt><dd>a numeric vector</dd>
 <dt><code>V2</code></dt><dd>a numeric vector</dd>
 <dt><code>V3</code></dt><dd>a numeric vector</dd>
 </dl>

Format

Simulated alternative splicing — simSplicing

A data frame with 5000 observations on the following 
9 variables.<dl class='dl-horizontal'>
 <dt><code>Isoform</code></dt><dd>a factor with levels</dd>
 <dt><code>geneid</code></dt><dd>a factor with levels</dd>
 <dt><code>label</code></dt><dd>a numeric vector</dd>
 <dt><code>D1</code></dt><dd>a numeric vector</dd>
 <dt><code>D2</code></dt><dd>a numeric vector</dd>
 <dt><code>D3</code></dt><dd>a numeric vector</dd>
 <dt><code>V1</code></dt><dd>a numeric vector</dd>
 <dt><code>V2</code></dt><dd>a numeric vector</dd>
 <dt><code>V3</code></dt><dd>a numeric vector</dd>
 </dl>

simSplicing: Simulated alternative splicing

Description

Usage

Arguments

Format

Details

Examples