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cellHTS2 (version 2.36.0)

Analysis of cell-based screens - revised version of cellHTS

Description

This package provides tools for the analysis of high-throughput assays that were performed in microtitre plate formats (including but not limited to 384-well plates). The functionality includes data import and management, normalisation, quality assessment, replicate summarisation and statistical scoring. A webpage that provides a detailed graphical overview over the data and analysis results is produced. In our work, we have applied the package to RNAi screens on fly and human cells, and for screens of yeast libraries. See ?cellHTS2 for a brief introduction.

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Version

Version

2.36.0

License

Artistic-2.0

Homepage

http://www.dkfz.de/signaling

Maintainer

Joseph Barry

Last Published

February 15th, 2017

Functions in cellHTS2 (2.36.0)

A sample cellHTS object containing dual channel data

Generate the hit list from a scored cellHTS object

getMeasureRepAgreement

Measures of agreement between plate replicates from a cellHTS object

A sample cellHTS object - D. melanogaster genome-wide RNAi screen

Rearrange dataframe entries such that there is exactly one row per ID.

Creates an object of class "ROC" which can be plotted as a ROC curve

Access and replace the batch information of a cellHTS object

Access and replace the assayData slot of a cellHTS object

Class that contain data that can be plotted as a ROC curve.

Configures the plates and plate result files

Per-experiment Z'-factor of a cellHTS object

Retrieve information related with the format of a RNAi experiment

B score normalization

Sigmoidal transformation of the score values stored in a cellHTS object obtaining the call values for each probe.

Wrapper to function 'write.table' used to write data to a tab-delimited file

Access the annotation from a cellHTS object.

convertOldCellHTS

Convert an old S3 class cellHTS object to the new S4 class cellHTS object

getEnVisionRawData

Read a plate file obtain from EnVision Plate Reader

configurationAsScreenPlot

Screen plot of the plate configuration of a cellHTS object

convertWellCoordinates

Converts different well identifiers

cellHTS2 Package Overview

readHTAnalystData

Read a set of plate results obtained from a HTanalyser plate reader

A sample S3 class cellHTS object - D. melanogaster genome-wide RNAi screen

scoreReplicates

Scores normalized replicate values given in a cellHTS object

A sample cellHTS object - D. melanogaster genome-wide RNAi screen

Retrieve the contents of the input files used to generate a given cellHTS object.

Experiment-wide quality control plot of a cellHTS object

summarizeReplicates

Summarize between scored replicate values given in a cellHTS object to obtain a single value for each probe

Retrieve the state of a cellHTS object.

Perform RSA ranking on the screening results.

Annotates the reagents (probes) of a cellHTS object

Constructor for an object of class gseaModule

plotSpatialEffects

Plate plot with the row and column offsets estimated by the a spatial normalization method

cellHTS2 HTML report settings

Write the data from a cellHTS object to a tab-delimited file

Dataset with annotation of CG identifiers

A class for data from cell-based high-throughput assays performed in plate format.

getDynamicRange

Per-plate dynamic range of a cellHTS object

spatialNormalization

Spatial normalization

Access plate effects stored in a cellHTS object.

Update old serialized cellHTS objects.

Build a cellHTS2 object from a data frame containing measurements

Read a collection of plate reader data files

normalizePlates

Per-plate data transformation, normalization and variance adjustment

Create a directory with HTML pages of linked tables and plots documenting the contents of a cellHTS experiment

templateDescriptionFile

Creates a template description file for an RNAi experiment

summarizeChannels

Summarization of dual-channel data