A B C D G I K L M N O P R S T U W
cellHTS2-package | cellHTS2 Package Overview |
annotate | Annotates the reagents (probes) of a cellHTS object |
annotate-method | Annotates the reagents (probes) of a cellHTS object |
batch | Access and replace the batch information of a cellHTS object |
batch-method | Access and replace the batch information of a cellHTS object |
batch<- | Access and replace the batch information of a cellHTS object |
batch<--method | Access and replace the batch information of a cellHTS object |
bdgpbiomart | Dataset with annotation of CG identifiers |
Bscore | B score normalization |
buildCellHTS2 | Build a cellHTS2 object from a data frame containing measurements |
cellHTS | A class for data from cell-based high-throughput assays performed in plate format. |
cellHTS-class | A class for data from cell-based high-throughput assays performed in plate format. |
cellHTS2 | cellHTS2 Package Overview |
class.cellHTS | A class for data from cell-based high-throughput assays performed in plate format. |
coerce-method | A class for data from cell-based high-throughput assays performed in plate format. |
compare2cellHTS | A class for data from cell-based high-throughput assays performed in plate format. |
compare2cellHTS-method | A class for data from cell-based high-throughput assays performed in plate format. |
configurationAsScreenPlot | Screen plot of the plate configuration of a cellHTS object |
configure | Configures the plates and plate result files |
configure-method | Configures the plates and plate result files |
convertOldCellHTS | Convert an old S3 class cellHTS object to the new S4 class cellHTS object |
convertWellCoordinates | Converts different well identifiers |
Data | Access and replace the assayData slot of a cellHTS object |
Data-method | Access and replace the assayData slot of a cellHTS object |
Data<- | Access and replace the assayData slot of a cellHTS object |
Data<--method | Access and replace the assayData slot of a cellHTS object |
dualCh | A sample cellHTS object containing dual channel data |
geneAnno | Access the annotation from a cellHTS object. |
geneAnno-method | Access the annotation from a cellHTS object. |
getDynamicRange | Per-plate dynamic range of a cellHTS object |
getEnVisionCrosstalkCorrectedData | Read a plate file obtain from EnVision Plate Reader |
getEnVisionRawData | Read a plate file obtain from EnVision Plate Reader |
getMeasureRepAgreement | Measures of agreement between plate replicates from a cellHTS object |
getSettings | cellHTS2 HTML report settings |
getTopTable | Generate the hit list from a scored cellHTS object |
getZfactor | Per-experiment Z'-factor of a cellHTS object |
gseaModule | Constructor for an object of class gseaModule |
imageScreen | Experiment-wide quality control plot of a cellHTS object |
initialize-method | A class for data from cell-based high-throughput assays performed in plate format. |
intensityFiles | Retrieve the contents of the input files used to generate a given cellHTS object. |
intensityFiles-method | Retrieve the contents of the input files used to generate a given cellHTS object. |
KcViab | A sample cellHTS object - D. melanogaster genome-wide RNAi screen |
KcViabSmall | A sample cellHTS object - D. melanogaster genome-wide RNAi screen |
length-method | Constructor for an object of class gseaModule |
lines-method | Creates an object of class "ROC" which can be plotted as a ROC curve |
meanSdPlot | A class for data from cell-based high-throughput assays performed in plate format. |
meanSdPlot-method | A class for data from cell-based high-throughput assays performed in plate format. |
name | A class for data from cell-based high-throughput assays performed in plate format. |
name-method | A class for data from cell-based high-throughput assays performed in plate format. |
name<- | A class for data from cell-based high-throughput assays performed in plate format. |
name<--method | A class for data from cell-based high-throughput assays performed in plate format. |
nbatch | A class for data from cell-based high-throughput assays performed in plate format. |
nbatch-method | A class for data from cell-based high-throughput assays performed in plate format. |
normalizePlates | Per-plate data transformation, normalization and variance adjustment |
oldKcViabSmall | A sample S3 class cellHTS object - D. melanogaster genome-wide RNAi screen |
oneRowPerId | Rearrange dataframe entries such that there is exactly one row per ID. |
pdim | Retrieve information related with the format of a RNAi experiment |
pdim-method | Retrieve information related with the format of a RNAi experiment |
plate | Retrieve information related with the format of a RNAi experiment |
plate-method | Retrieve information related with the format of a RNAi experiment |
plateConf | Retrieve the contents of the input files used to generate a given cellHTS object. |
plateConf-method | Retrieve the contents of the input files used to generate a given cellHTS object. |
plateEffects | Access plate effects stored in a cellHTS object. |
plateEffects-method | Access plate effects stored in a cellHTS object. |
plateList | Retrieve the contents of the input files used to generate a given cellHTS object. |
plateList-method | Retrieve the contents of the input files used to generate a given cellHTS object. |
plot-method | Creates an object of class "ROC" which can be plotted as a ROC curve |
plotSpatialEffects | Plate plot with the row and column offsets estimated by the a spatial normalization method |
position | Retrieve information related with the format of a RNAi experiment |
position-method | Retrieve information related with the format of a RNAi experiment |
readHTAnalystData | Read a set of plate results obtained from a HTanalyser plate reader |
readPlateList | Read a collection of plate reader data files |
ROC | Creates an object of class "ROC" which can be plotted as a ROC curve |
ROC-class | Class that contain data that can be plotted as a ROC curve. |
ROC-method | Creates an object of class "ROC" which can be plotted as a ROC curve |
rsa | Perform RSA ranking on the screening results. |
scoreReplicates | Scores normalized replicate values given in a cellHTS object |
scores2calls | Sigmoidal transformation of the score values stored in a cellHTS object obtaining the call values for each probe. |
screenDesc | Retrieve the contents of the input files used to generate a given cellHTS object. |
screenDesc-method | Retrieve the contents of the input files used to generate a given cellHTS object. |
screenLog | Retrieve the contents of the input files used to generate a given cellHTS object. |
screenLog-method | Retrieve the contents of the input files used to generate a given cellHTS object. |
setSettings | cellHTS2 HTML report settings |
settings | cellHTS2 HTML report settings |
show-method | Class that contain data that can be plotted as a ROC curve. |
show-method | A class for data from cell-based high-throughput assays performed in plate format. |
spatialNormalization | Spatial normalization |
state | Retrieve the state of a cellHTS object. |
state-method | Retrieve the state of a cellHTS object. |
summarizeChannels | Summarization of dual-channel data |
summarizeReplicates | Summarize between scored replicate values given in a cellHTS object to obtain a single value for each probe |
templateDescriptionFile | Creates a template description file for an RNAi experiment |
updateCellHTS | Update old serialized cellHTS objects. |
well | Retrieve information related with the format of a RNAi experiment |
well-method | Retrieve information related with the format of a RNAi experiment |
wellAnno | Access the annotation from a cellHTS object. |
wellAnno-method | Access the annotation from a cellHTS object. |
write.tabdel | Wrapper to function 'write.table' used to write data to a tab-delimited file |
writeReport | Create a directory with HTML pages of linked tables and plots documenting the contents of a cellHTS experiment |
writeTab | Write the data from a cellHTS object to a tab-delimited file |
writeTab-method | Write the data from a cellHTS object to a tab-delimited file |