countMat

<p>A data frame with 1609 individual screened genes and 100 functional readouts. The data was generated from a siRNA screen for global splicing regulators. In this screen, we interrogated ~400 endogenous alternative splicing (AS) events by using an oligo ligation-based strategy to quantify 18,480 pools of siRNAs against annotated protein-coding genes in the human genome.</p>

datasets

The advent of genomic technologies has enabled the generation of two-dimensional or even multi-dimensional high-throughput data, e.g., monitoring multiple changes in gene expression in genome-wide siRNA screens across many different cell types (E Robert McDonald 3rd (2017) <doi: 10.1016/j.cell.2017.07.005> and Tsherniak A (2017) <doi: 10.1016/j.cell.2017.06.010>) or single cell transcriptomics under different experimental conditions. We found that simple computational methods based on a single statistical criterion is no longer adequate for analyzing such multi-dimensional data. We herein introduce 'ZetaSuite', a statistical package initially designed to score hits from two-dimensional RNAi screens.We also illustrate a unique utility of 'ZetaSuite' in analyzing single cell transcriptomics to differentiate rare cells from damaged ones (Vento-Tormo R (2018) <doi: 10.1038/s41586-018-0698-6>). In 'ZetaSuite', we  have the following steps: QC of input datasets, normalization using Z-transformation, Zeta score calculation and hits selection based on defined Screen Strength.

Junhui Li

ZetaSuite

Analyze High-Dimensional High-Throughput Dataset and Quality
Control Single-Cell RNA-Seq

Yajing Hao

Shuyang Zhang

Guofeng Zhao

Xiang-Dong Fu

countMat function

<p>A data frame with 1609 observations on the following 100 variables</p><dl>
    A data frame with 1609 observations on the following 100 maker variables.Each row represents gene with specific knocking-down siRNA pool, each column is an AS event. The values in the matrix are the processed foldchange values between included exons and skipping exons read counts. 
  
</dl>


Format

Subsampled data from in-house HTS2 screening for global splicing regulators. — countMat

Subsampled data from in-house HTS2 screening for global splicing regulators.

countMat: Subsampled data from in-house HTS2 screening for global splicing regulators.

Description

Usage

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