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cellHTS (version 1.42.0)
Analysis of cell-based screens
Description
Analysis of cell-based RNA interference screens.
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Version
Version
1.42.0
1.40.2
1.38.0
1.36.0
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Version
1.42.0
License
Artistic-2.0
Homepage
http://www.dkfz.de/signaling
Maintainer
Andrzej Ole
Last Published
January 1st, 1970
Functions in cellHTS (1.42.0)
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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