Learn R Programming

cellHTS (version 1.42.0)

Analysis of cell-based screens

Description

Analysis of cell-based RNA interference screens.

Copy Link

Version

Version

1.42.0

License

Artistic-2.0

Maintainer

Andrzej Ole

Last Published

February 15th, 2017

Functions in cellHTS (1.42.0)

plotPlateLibrary

Plate plot of the raw data of the four consecutive 96-well plates of a given 384-well plate
ROC

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

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

Normalization and transformation of dual-channel data
Bscore

B score normalization
KcViab

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

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

Access plate effects stored in a cellHTS object.
getMatrix

Create a matrix with replicate data in columns
Data

Access and replace the assayData slot of a cellHTS object
writeTab

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

Read a collection of plate reader data files
updateCellHTS

Update old serialized cellHTS objects.
spatialNormalization

Spatial normalization
plotSpatialEffects

Plate plot with the row and column offsets estimated by the B score method
screenMatch

Matching the gene annotation of two screens
configure

Configures the plates and plate result files
readPlateData

Read a collection of plate reader data files
getEnVisionRawData

Read a plate file obtain from EnVision Plate Reader
KcViabSmall

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

Experiment-wide quality control plot of a cellHTS object
getTopTable

Generate the hit list from a scored cellHTS object
buildCellHTS2

Build a cellHTS2 object from a data frame containing measurements
getLibraryPlate

384-well plate assay format to a 96-well plate library format
annotate

Annotates the gene IDs of a given cellHTS object
scores2calls

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

Constructor for an object of class gseaModule
cellHTS-class

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

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

Access and replace the batch information of a cellHTS object
bdgpbiomart

Dataset with annotation of CG identifiers
oldKcViabSmall

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

Summarizes between normalized replicate values given in a cellHTS object, obtaining a single z-score for each probe
convertWellCoordinates

Converts different well identifiers
settings

cellHTS2 HTML report settings
dualCh

A sample cellHTS object containing dual channel data
state

Retrieve the state of a cellHTS object.
normalizeChannels

Normalization of dual-channel data and data transformation
cellHTS2

cellHTS2 Package Overview
plate

Retrieve information related with the format of a RNAi experiment
convertOldCellHTS

Convert an old S3 class cellHTS object to the new S4 class cellHTS object
write.tabdel

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

Printing cellHTS objects
oneRowPerId

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

Access the annotation from a cellHTS object.
configurationAsScreenPlot

Screen plot of the plate configuration of a cellHTS object
templateDescriptionFile

Creates a template description file for an RNAi experiment
getDynamicRange

Per-plate dynamic range of a cellHTS object
getMeasureRepAgreement

Measures of agreement between plate replicates from a cellHTS object
intensityFiles

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

Per-experiment Z'-factor of a cellHTS object
normalizePlates

Plate-wise data normalization, and data transformation
rsa

Perform RSA ranking on the screening results.
scoreReplicates

Scores normalized replicate values given in a cellHTS object