A B C D E F G H I L M N P Q R S T misc
CAGEr-package | Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining |
aggregateTagClusters | Aggregate TCs across all samples |
aggregateTagClusters-method | Aggregate TCs across all samples |
annotateConsensusClusters | Annotate and compute summary statistics |
annotateConsensusClusters-method | Annotate and compute summary statistics |
annotateCTSS | Annotate and compute summary statistics |
annotateCTSS-method | Annotate and compute summary statistics |
bam2CTSS | bam2CTSS |
CAGEexp | CAGEr class to hold all data and metadata about one CAGE experiment. |
CAGEexp-class | CAGEr class to hold all data and metadata about one CAGE experiment. |
CAGEr | CAGEr objects |
CAGEr-class | CAGEr objects |
CAGEr_Multicore | Multicore support in CAGEr |
CAGEset | Class '"CAGEset"' |
CAGEset-class | Class '"CAGEset"' |
CCdataframe2granges | Private functions to convert CC formats |
CCgranges2dataframe | Private functions to convert CC formats |
clusterCTSS | Cluster CTSSs into tag clusters |
clusterCTSS-method | Cluster CTSSs into tag clusters |
coerce-method | CAGEr class to hold all data and metadata about one CAGE experiment. |
coerce-method | Class '"CAGEset"' |
coerceInBSgenome | coerceInBSgenome |
consensusClusterConvertors | Private functions to convert CC formats |
ConsensusClusters | Classes for type safety. |
consensusClusters | Get or set consensus clusters from CAGEr objects |
consensusClusters-method | Get or set consensus clusters from CAGEr objects |
consensusClusters<- | Get or set consensus clusters from CAGEr objects |
consensusClusters<--method | Get or set consensus clusters from CAGEr objects |
consensusClustersDESeq2 | Export _consensus cluster_ expression data for DESeq2 analysis |
consensusClustersDESeq2-method | Export _consensus cluster_ expression data for DESeq2 analysis |
consensusClustersGR | Get or set consensus clusters from CAGEr objects |
consensusClustersGR-method | Get or set consensus clusters from CAGEr objects |
consensusClustersGR<- | Get or set consensus clusters from CAGEr objects |
consensusClustersGR<--method | Get or set consensus clusters from CAGEr objects |
consensusClustersQuantile | Quantile metadata stored in CAGEr objects. |
consensusClustersQuantile-method | Quantile metadata stored in CAGEr objects. |
consensusClustersQuantileLow | Quantile metadata stored in CAGEr objects. |
consensusClustersQuantileLow-method | Quantile metadata stored in CAGEr objects. |
consensusClustersQuantileLow<- | Quantile metadata stored in CAGEr objects. |
consensusClustersQuantileLow<--method | Quantile metadata stored in CAGEr objects. |
consensusClustersQuantileUp | Quantile metadata stored in CAGEr objects. |
consensusClustersQuantileUp-method | Quantile metadata stored in CAGEr objects. |
consensusClustersQuantileUp<- | Quantile metadata stored in CAGEr objects. |
consensusClustersQuantileUp<--method | Quantile metadata stored in CAGEr objects. |
consensusClustersSE | Get or set consensus clusters from CAGEr objects |
consensusClustersSE-method | Get or set consensus clusters from CAGEr objects |
consensusClustersSE<- | Get or set consensus clusters from CAGEr objects |
consensusClustersSE<--method | Get or set consensus clusters from CAGEr objects |
consensusClustersTpm | Extracting consensus clusters tpm matrix from CAGEset object |
consensusClustersTpm-method | Extracting consensus clusters tpm matrix from CAGEset object |
coverage-functions | Private functions behind 'cumulativeCTSSdistribution' |
CTSS | Classes for type safety. |
CTSS-class | Classes for type safety. |
CTSS.chr | Classes for type safety. |
CTSS.chr-class | Classes for type safety. |
CTSSclusteringMethod | Get /set CTSS clustering method |
CTSSclusteringMethod-method | Get /set CTSS clustering method |
CTSSclusteringMethod<- | Get /set CTSS clustering method |
CTSSclusteringMethod<--method | Get /set CTSS clustering method |
CTSScoordinates | Genomic coordinates of TSSs from a 'CAGEr' object |
CTSScoordinates-method | Genomic coordinates of TSSs from a 'CAGEr' object |
CTSScoordinatesGR | Genomic coordinates of TSSs from a 'CAGEr' object |
CTSScoordinatesGR-method | Genomic coordinates of TSSs from a 'CAGEr' object |
CTSScoordinatesGR<- | Genomic coordinates of TSSs from a 'CAGEr' object |
CTSScoordinatesGR<--method | Genomic coordinates of TSSs from a 'CAGEr' object |
CTSScumulativesCC | Get/set CTSS cumulative TC or CC data |
CTSScumulativesCC-method | Get/set CTSS cumulative TC or CC data |
CTSScumulativesTagClusters | Get/set CTSS cumulative TC or CC data |
CTSScumulativesTagClusters-method | Get/set CTSS cumulative TC or CC data |
CTSScumulativesTagClusters<- | Get/set CTSS cumulative TC or CC data |
CTSScumulativesTagClusters<--method | Get/set CTSS cumulative TC or CC data |
CTSSnormalizedTpm | Extracting normalized CAGE signal for TSSs from CAGEr objects |
CTSSnormalizedTpm-method | Extracting normalized CAGE signal for TSSs from CAGEr objects |
CTSSnormalizedTpmDF | Extracting normalized CAGE signal for TSSs from CAGEr objects |
CTSSnormalizedTpmDf | Extracting normalized CAGE signal for TSSs from CAGEr objects |
CTSSnormalizedTpmDF-method | Extracting normalized CAGE signal for TSSs from CAGEr objects |
CTSSnormalizedTpmDf-method | Extracting normalized CAGE signal for TSSs from CAGEr objects |
CTSSnormalizedTpmGR | Extracting normalized CAGE signal for TSSs from CAGEr objects |
CTSSnormalizedTpmGR-method | Extracting normalized CAGE signal for TSSs from CAGEr objects |
CTSStagCount | Extract raw CAGE TSSs expression tables from 'CAGEr' objects |
CTSStagCount-method | Extract raw CAGE TSSs expression tables from 'CAGEr' objects |
CTSStagCountDA | Extract raw CAGE TSSs expression tables from 'CAGEr' objects |
CTSStagCountDA-method | Extract raw CAGE TSSs expression tables from 'CAGEr' objects |
CTSStagCountDF | Extract raw CAGE TSSs expression tables from 'CAGEr' objects |
CTSStagCountDf | Extract raw CAGE TSSs expression tables from 'CAGEr' objects |
CTSStagCountDF-method | Extract raw CAGE TSSs expression tables from 'CAGEr' objects |
CTSStagCountDf-method | Extract raw CAGE TSSs expression tables from 'CAGEr' objects |
CTSStagCountGR | Extract raw CAGE TSSs expression tables from 'CAGEr' objects |
CTSStagCountGR-method | Extract raw CAGE TSSs expression tables from 'CAGEr' objects |
CTSStagCountSE | Extract raw CAGE TSSs expression tables from 'CAGEr' objects |
CTSStagCountSE-method | Extracting CAGE tag count for TSSs from CAGEr objects |
CTSStagCountSE<- | Genomic coordinates of TSSs from a 'CAGEr' object |
CTSStagCountSE<--method | Genomic coordinates of TSSs from a 'CAGEr' object |
CTSStagCountTable | Extracting CAGE tag count for TSSs from CAGEr objects |
CTSStagCountTable-method | Extracting CAGE tag count for TSSs from CAGEr objects |
CTSStoGenes | Make a gene expression table. |
CTSStoGenes-method | Make a gene expression table. |
cumulativeCTSSdistribution | Cumulative sums of CAGE counts along genomic regions |
cumulativeCTSSdistribution-method | Cumulative sums of CAGE counts along genomic regions |
CustomConsensusClusters | Expression levels of consensus cluster |
CustomConsensusClusters-method | Expression levels of consensus cluster |
distclu-functions | Private functions for distance clustering. |
exampleCAGEexp | Example CAGEexp object. |
exampleCAGEset | Example CAGEset object with zebrafish CAGE data |
exampleZv9_annot | Example zebrafish annotation data |
exportCTSStoBedGraph | Creating bedGraph/bigWig tracks of CAGE transcription starts sites |
exportCTSStoBedGraph-method | Creating bedGraph/bigWig tracks of CAGE transcription starts sites |
exportToBed | Create BED tracks of TSSs and clusters of TSSs |
exportToBed-method | Create BED tracks of TSSs and clusters of TSSs |
expressionClasses | Extract labels of expression classes |
expressionClasses-method | Extract labels of expression classes |
extractExpressionClass | Extract elements of the specified expression class |
extractExpressionClass-method | Extract elements of the specified expression class |
FANTOM5humanSamples | List of FANTOM5 human CAGE samples |
FANTOM5mouseSamples | List of FANTOM5 mouse CAGE samples |
findStrandInvaders | Detect and remove strand invasion artefacts |
findStrandInvaders-method | Detect and remove strand invasion artefacts |
GeneExpDESeq2 | Export gene expression data for DESeq2 analysis |
GeneExpDESeq2-method | Export gene expression data for DESeq2 analysis |
GeneExpSE | Retreives the SummarizedExperiment containing gene expression levels. |
GeneExpSE-method | Retreives the SummarizedExperiment containing gene expression levels. |
genomeName | Extracting genome name from CAGEr objects |
genomeName-method | Extracting genome name from CAGEr objects |
genomeName<- | Extracting genome name from CAGEr objects |
genomeName<--method | Extracting genome name from CAGEr objects |
getCTSS | Reading CAGE data from input file(s) and detecting TSSs |
getCTSS-method | Reading CAGE data from input file(s) and detecting TSSs |
getExpressionProfiles | CAGE data based expression clustering |
getExpressionProfiles-method | CAGE data based expression clustering |
getShiftingPromoters | Select consensus clusters with shifting score above threshold |
getShiftingPromoters-method | Select consensus clusters with shifting score above threshold |
hanabi | Calcultate richness in preparation for plotting |
hanabi-class | Hanabi class |
hanabi-method | Calcultate richness in preparation for plotting |
hanabiPlot | hanabiPlot |
import.bam | import.bam |
import.bam.ctss | import.bam.ctss |
import.bedCTSS | import.bedCTSS |
import.bedmolecule | import.bedmolecule |
import.bedScore | import.bedScore |
import.CAGEscanMolecule | import.CAGEscanMolecule |
import.CTSS | import.CTSS |
importPublicData | Importing publicly available CAGE data from various resources |
importPublicData-method | Importing publicly available CAGE data from various resources |
inputFiles | Extracting paths to input files from CAGEr objects |
inputFiles-method | Extracting paths to input files from CAGEr objects |
inputFiles<- | Extracting paths to input files from CAGEr objects |
inputFiles<--method | Extracting paths to input files from CAGEr objects |
inputFilesType | Input file formats for CAGEr objects |
inputFilesType-method | Input file formats for CAGEr objects |
inputFilesType<- | Input file formats for CAGEr objects |
inputFilesType<--method | Input file formats for CAGEr objects |
librarySizes | Extracting library sizes from CAGEr objects |
librarySizes-method | Extracting library sizes from CAGEr objects |
lines.hanabi | Plotting Hanabi objects |
loadFileIntoGPos | loadFileIntoGPos |
mapStats | Process mapping statistics |
mapStatsScopes | mapStats scopes |
mergeCAGEsets | Merge two CAGEr objects into one |
mergeCAGEsets-method | Merge two CAGEr objects into one |
mergeSamples | Merge CAGE samples |
mergeSamples-method | Merge CAGE samples |
moleculesGR2CTSS | moleculesGR2CTSS |
msScope_all | mapStats scopes |
msScope_annotation | mapStats scopes |
msScope_counts | mapStats scopes |
msScope_mapped | mapStats scopes |
msScope_qc | mapStats scopes |
msScope_steps | mapStats scopes |
normalizeTagCount | Normalizing raw CAGE tag count |
normalizeTagCount-method | Normalizing raw CAGE tag count |
parseCAGEscanBlocksToGrangeTSS | parseCAGEscanBlocksToGrangeTSS |
plot.hanabi | Plotting Hanabi objects |
plotAnnot | Plot annotation statistics |
plotAnnot-method | Plot annotation statistics |
plotCorrelation | Pairwise scatter plots and correlations of CAGE signal |
plotCorrelation-method | Pairwise scatter plots and correlations of CAGE signal |
plotCorrelation2 | Pairwise scatter plots and correlations of CAGE signal |
plotCorrelation2-method | Pairwise scatter plots and correlations of CAGE signal |
plotExpressionProfiles | Plotting expression profiles derived from CAGE data |
plotExpressionProfiles-method | Plotting expression profiles derived from CAGE data |
plotInterquantileWidth | Plot cluster widths |
plotInterquantileWidth-method | Plot cluster widths |
plotReverseCumulatives | Plot reverse cumulative number of CAGE tags per CTSS |
plotReverseCumulatives-method | Plot reverse cumulative number of CAGE tags per CTSS |
points.hanabi | Plotting Hanabi objects |
quantilePositions | Determine CTSS quantile positions within clusters |
quantilePositions-method | Determine CTSS quantile positions within clusters |
ranges2annot | hierarchical annotation of CTSSes |
ranges2genes | ranges2genes |
ranges2names | ranges2names |
removeStrandInvaders | Detect and remove strand invasion artefacts |
removeStrandInvaders-method | Detect and remove strand invasion artefacts |
sampleLabels | Get and set sample labels |
sampleLabels-method | Get and set sample labels |
sampleLabels<- | Get and set sample labels |
sampleLabels<--method | Get and set sample labels |
sampleList | Get and set sample labels |
sampleList-method | Get and set sample labels |
scoreShift | Calculate promoter shifting score |
scoreShift-method | Calculate promoter shifting score |
seqNameTotalsSE | Retreives the SummarizedExperiment containing chromosome expression totals. |
seqNameTotalsSE-method | Retreives the SummarizedExperiment containing chromosome expression totals. |
seqNameTotalsSE<- | Retreives the SummarizedExperiment containing chromosome expression totals. |
setColors | Set colors for samples |
setColors-method | Set colors for samples |
show-method | Methods for function 'show' |
show-methods | Methods for function 'show' |
Strand invaders | Detect and remove strand invasion artefacts |
summariseChrExpr | Expression levels by chromosomes |
summariseChrExpr-method | Expression levels by chromosomes |
tagClusterConvertors | Private functions to convert TC formats |
TagClusters | Classes for type safety. |
tagClusters | Extract tag clusters (TCs) for individual CAGE experiments |
tagClusters-method | Extract tag clusters (TCs) for individual CAGE experiments |
tagClustersGR | Extract tag clusters (TCs) for individual CAGE experiments |
tagClustersGR-method | Extract tag clusters (TCs) for individual CAGE experiments |
tagClustersGR<- | Extract tag clusters (TCs) for individual CAGE experiments |
tagClustersGR<--method | Extract tag clusters (TCs) for individual CAGE experiments |
tagClustersQuantile | Quantile metadata stored in CAGEr objects. |
tagClustersQuantile-method | Quantile metadata stored in CAGEr objects. |
tagClustersQuantileLow | Quantile metadata stored in CAGEr objects. |
tagClustersQuantileLow-method | Quantile metadata stored in CAGEr objects. |
tagClustersQuantileLow<- | Quantile metadata stored in CAGEr objects. |
tagClustersQuantileLow<--method | Quantile metadata stored in CAGEr objects. |
tagClustersQuantileUp | Quantile metadata stored in CAGEr objects. |
tagClustersQuantileUp-method | Quantile metadata stored in CAGEr objects. |
tagClustersQuantileUp<- | Quantile metadata stored in CAGEr objects. |
tagClustersQuantileUp<--method | Quantile metadata stored in CAGEr objects. |
TCdataframe2granges | Private functions to convert TC formats |
TCgranges2dataframe | Private functions to convert TC formats |
.byCtss | Apply functions to identical CTSSes. |
.byCtss-method | Apply functions to identical CTSSes. |
.cluster.ctss.chr | Private functions for distance clustering. |
.cluster.ctss.strand | Private functions for distance clustering. |
.clusterAggregateAndSum | Aggregate identical clusters and sum their scores. |
.clusterAggregateAndSum-method | Aggregate identical clusters and sum their scores. |
.ConsensusClusters | Classes for type safety. |
.CTSS | Classes for type safety. |
.CTSS.chr | Classes for type safety. |
.ctss2clusters | Private functions for distance clustering. |
.distclu | Private functions for distance clustering. |
.get.quant.pos | Get quantile positions |
.getCAGEsignalCoverage | Private functions behind 'cumulativeCTSSdistribution' |
.getCumsum | Private functions behind 'cumulativeCTSSdistribution' |
.getCumsumChr2 | Private functions behind 'cumulativeCTSSdistribution' |
.hanabi | Hanabi class |
.powerLaw | .powerLaw |
.summarize.clusters | Private functions for distance clustering. |
.TagClusters | Classes for type safety. |