Man pages for uzh/ezRun
An R meta-package for the analysis of Next Generation Sequencing Data

addCountResultSummaryAdds a summary of the count result
addDatasetAdds a dataset
addDEXSeqConditionAddition experimental conditions to input files
addGageTablesAdds the gage tables
addJavaScriptIgvStarterAdds a java function
addQcScatterPlotsAdds QC scatter plots
addResultFileAdds a result file
addSignificantCountsAdds tables of the significant counts
addTestScatterPlotsAdds test scatter plots
addTranscriptsToGffExonsAdds transcripts from exons to the annotation
addTxtLinksToReportAdds text links
aggregateCountsByGeneAggregates counts by gene
annotatePeaksAnnotates peaks
averageColumnsAverages columns together
averageRowsAverages rows together
bam2bwBam to bigwig
bam2fastqBam/Sam file to fastq file conversion
calmdBamCalculate MD tag for BAM
cleanGenomeFilesCleans genome files
cleanupMultiGroupsInputCleans up input from the edgeR multi groups app
cleanupTwoGroupsInputCleans up input from two group apps
clusterHeatmapPlots the cluster heatmap
CollectAlignmentSummaryMetricsCollectAlignmentSummaryMetrics
CollectRnaSeqMetricsCollectRnaSeqMetrics
colorClusterLabelsGets the color cluster labels
computeBamStatsComputes the BAM statistics
computeRangeStatsComputes stats of genomic ranges
consensusPeaksGet consensus peaks
convertGtfToGffConvert annotation file from GTF format to GFF
countDensPlotPlots the count densities
countReadsInFastqCounts reads in FastQ files
doGoDo GO?
dupBamDuplicates operation in bam
DuplicationMetricsDuplicationMetrics
enrichrAddListAdd gene list
enrichrEnrichEnrichment analysis
expandGRangesExpands genomic ranges
ezAllPairScatterDoes scatter plots of all pairs
EzAppBamPreview-classThe R5 class representing a runnable app using...
EzAppBismark-classThe R5 class representing a runnable app using...
EzAppBowtie2-classThe R5 class representing a runnable app using...
EzAppBowtie2Transcriptome-classThe R5 class representing a runnable app using...
EzAppBowtie-classThe R5 class representing a runnable app using...
EzAppBWA-classThe R5 class representing a runnable app using...
EzAppCanu-classThe R5 class representing a runnable app using...
EzAppChipStats-classThe R5 class representing a runnable app using...
EzApp-classThe R5 class representing a runnable app
EzAppCountOverlaps-classThe R5 class representing a runnable app using...
EzAppCountQC-classThe R5 class representing a runnable app using...
EzAppDeseq2-classThe R5 class representing a runnable app using...
EzAppDEXSeqAnalysis-classThe R5 class representing a runnable app using...
EzAppEdger-classThe R5 class representing a runnable app using...
EzAppEdgerMulti-classThe R5 class representing a runnable app using...
EzAppFastqc-classThe R5 class representing a runnable app using...
EzAppFastqScreen-classThe R5 class representing a runnable app using...
EzAppFeatureCountsFeatureCounts App
EzAppFeatureCounts-classThe R5 class representing a runnable app using...
EzAppFlash-classThe R5 class representing a runnable app using...
EzAppGatkDnaHaplotyper-classThe R5 class representing a runnable app using...
EzAppGatkRnaHaplotyper-classThe R5 class representing a runnable app using...
EzAppHGAP-classThe R5 class representing a runnable app using...
EzAppJoinGenoTypes-classThe R5 class representing a runnable app using...
EzAppKallisto-classThe R5 class representing a runnable app using...
EzAppMacs2-classThe R5 class representing a runnable app using...
EzAppMEME-classThe R5 class representing a runnable app using...
EzAppMpileup-classThe R5 class representing a runnable app using...
EzAppNcpro-classThe R5 class representing a runnable app using...
EzAppQuast-classThe R5 class representing a runnable app using...
EzAppResequencing-classThe R5 class representing a runnable app using...
EzAppRnaBamStats-classThe R5 class representing a runnable app using...
EzAppRSEM-classThe R5 class representing a runnable app using...
EzAppSalmon-classThe R5 class representing a runnable app using...
EzAppScater-classThe R5 class representing a runnable app using...
EzAppSCCounts-classThe R5 class representing a runnable app using...
EzAppSpades-classThe R5 class representing a runnable app using...
EzAppSplitAndCluster-classThe R5 class representing a runnable app using...
EzAppSTAR-classThe R5 class representing a runnable app using...
EzAppSubreads-classThe R5 class representing a runnable app using...
EzAppTeqc-classThe R5 class representing a runnable app using...
EzAppTophat-classThe R5 class representing a runnable app using...
EzAppTranscriptCoverage-classThe R5 class representing a runnable app using...
EzAppTrinity-classThe R5 class representing a runnable app using...
ezBam2bigwigConverts from bam to bigwig
ezBamSeqNamesGets sequence names
ezBuildAttributeFieldBuilds an annotation attributes field
ezChromSizesFromVcfGets chromosome sizes from a VCF file
ezCollapseCollapses a vector in a single character
ezColorLegendPlots a color scale
ezCombineReadDatasetsCombine the reads from two datasets in a single dataset
ezCorrelationPlotDoes a correlation plot
ezCutConvert numeric to factor
EzDataset-classThe R5 class representing a dataset
ezDesignFromDatasetGets the design from the dataset
ezDuplicatedWhich values are duplicated?
ezFilterVcfFilters a VCF file and writes it back
ezFlexTableWrapper for 'FlexTable()'
ezFrameWrapper for data.frame suitable for data processing rather...
ezGeomeanGeometric mean
ezGreplMatches patterns and returns a logical vector
ezGroupGOGroups GO terms and information
ezHeadWrites the head of a file
ezHeatmapPlots a heatmap
ezImageFileLinkGets an image link as html
ezInteractiveTableSaves an interactive table
ezIntStringFormat an integer into a character using only digits
ezIsAbsolutePathIs x an absolute file path?
ezIsSpecifiedCheck if a value is specified
ezJobStartWrites start time of job
ezLegendPlots a legend
ezLoadFeaturesLoads annotation features from a file
ezLogmeanNormScales columns of a matrix to logarithmic mean
ezMailMails information, the nodename and working directory
ezMatrixCreates a matrix
ezMclapplyParallel version of 'lapply()'
ezMdsPlotPlots the multi dimensional scaling
ezMedianNormScales columns of a matrix to median
ezMethodDEXSeqAnalysisRunMethod for reference class EzAppDEXSeqAnalysis
ezMethodSubsampleReadsSubsample reads in a fastq dataset file
ezMethodTrimTrims input reads
ezMultiplicatedWhich values occur at least 'n' times?
ezNormNormalization
ezParamBuild parameter object
ezPresentFlagsWhich values to keep?
ezQuantileNormQuantile Normalization
ezReadGappedAlignmentsReads gapped alignments from bam
ezReadGffReads an annotation table from a file.
ezReadPairedAlignmentsReads paired alignments from bam
ezRead.tableModified version of read.table
EzRef-classThe S4 class representing a collection of information about...
ezReplicateNumberCount how often a value has been seen before
EzResult-classThe object that represents a result of an expression analysis
ezRun-packagea meta-package that integrates NGS related R-packages and...
ezScaleColumnsScales columns of a matrix
ezScanBamScans a bam file
ezScatterDoes scatter plots
ezSessionInfoSaves session info in a .txt file
ezSmoothScatterDoes smooth scatter plots
ezSortIndexBamSorts and indexes a bam file
ezSplitSeparates a character vector into a matrix by splitting it.
ezSplitLongLabelsSplits long labels into two lines
ezSystemInvokes a system command
ezThreadsDetermines the number of CPU cores to be used
ezTimeModified version of Sys.time()
ezTranscriptDbFromRefGets the transcripts database from the reference
ezUtrSequencesGets UTR sequences
ezValidFilenameEnforces a valid file name
ezValidMailIs the email-address valid?
ezVolcanoVolcano plot
ezVsnNormVariance Stabilizing Normalization
ezWriteWrite in a single line
ezWriteElapsedWrites elapsed time of job
ezWrite.tableModified version of write.table
ezXYScatter.2XYScatter plot
fastqs2bamFastq files to Bam with RG tag
featAnnoIOFeature annotation file IO.
filterEnrichrResultsResult filtering
filterFastqByBamFilters FastQ files by bam
filteroutBamFilter bam
fixStrandFixes the strand information
gageSigGenesGets significant genes
getBamMultiMatchingGets bam multi matching
getBlacklistedRegionsGet blacklisted genomic regions
getBlueRedScaleGets a color scale from blue to red
getBowtie2ReferenceBuilds and gets a Bowtie2 reference
getBowtie2TranscriptomeReferenceBuilds and gets a Bowtie2 reference
getBowtieReferenceBuilds and gets a Bowtie reference
getBWAReferenceBuilds and gets a BWA reference
getDupRateFromBamDuplication rate from Bam of RNA-Seq.
getEnrichrLibNamesGet Enrichr library names
getEnsemblTypesGets the ensembl types
getExonNumberGets the exon numbers
getGeneIdExprLinksGet Links from GeneIds to Expression result files
getGeneMappingGets the isoform-to-gene mapping
getGeneSetsGets the gene set
getGeneTableGenerate gene table from DEXSeqResults object
getGOparentsGets the GO parents
getIgvLocusLinkGets an IGV locus link in .html format
getKallistoReferenceBuilds and gets a kallisto reference
getKeggIdGets the KEGG ID
getQualityMatrixGet quality matrix
getRangeValuesGets the values of genomic ranges
getReferenceFeaturesBedGets a bed file
getRpkmGets measurements from rawData
getRSEMReferenceBuilds and gets a RSEM reference
getSalmonReferenceBuilds and gets a salmon reference
getSampleColorsGets the sample colors
getSpeciesNameGets the species name
getSTARReferenceBuilds and gets a STAR reference
getSuffixGets the suffix of a file name
getTranscript2GeneGets gene names from annotation
getTranscriptCoverageGets transcripts coverage
getTranscriptGcAndWidthGets GC proportions and gene widths
getTranscriptSequencesGets transcript sequences
getTuxedoLibraryTypeGets the tuxedo library type
gffToRangesGets GRanges from annotation
gffTrimTranscriptsTrims transcripts in annotation data.frames
gffUtilitiesgff utilities functions
goClusterTableGets the GO cluster table
goStringsToListParses GO strings to a list
groupGffGroups annotation
hasFilesafeCharactersChecks if the argument can be safely used as a filename
imgLinksPastes image links as html
import.Macs2PeaksImport the MACS2 peak file
interleaveMatricesByColumnCombines two matrices by their columns
intHistShrinks values and plots a histogram
inverseMappingInverse mapping
isErrorTests if x contains an error
isValidCigarIs 'x' a valid cigar?
lastValGets the last value of an object
lGetGlobalCountParamspecification of default values used for count splitting
lGetPyScriptPathsGet list with required python script paths
loadCountDatasetLoads the count dataset
loadSCCountDatasetLoads the count dataset of single cell experiment
logMessageLogs time and base directory together with a parameter
makeCoordinateMake a coordinate
makeMinimalSingleEndReadDatasetMakes a minimal single end dataset
mioStringConverts a number into a character representing millions
mkCurlQryStringQuery string generator
modifyInputinput is modified to show the count results
multiGroupCountComparisonCompares the counts of many groups
ncproAnalysis of small RNA sequences using ncpro
openBsdocReportOpens an html report
parseEnrichrLibNamesRetrieve Enrichr library names
plateStatisticsBias inspection per plate
plotBamStatPlots the BAM statistics
postProcessResultsPostprocessing counts produced as results from ncpro
readNcProResultReads NcPro results
runCountSingleBamRun counts for a single BAM file
runEnrichrRun Enrichr
runGageAnalysisRuns the gage analysis
runNgsCountQCRuns the NGS count QC
runTEQCRuns the target enrichment quality control
separateGoIdsByOntoSeparates GO ID's by ontology
setwdNewSwitches to a working directory
shiftZerosShifts zeros
shrinkToRangeShrink the dynamic range of a numeric vector, matrix, or data...
splitBamByRGSplit bam file
splitCoordinateSplits fragment coordinates
splitCountssplit count result into different files and put them into...
strandValueGets a strand value
subSampleRleSubsets an Rle object
tableFromSetsCreates a contingency table from a list of vectors.
transcriptAnnoFromGtfGets the transcript annotation
trimGRangestrim GRanges object
trimWhiteSpaceTrims white space
twoGroupCountComparisonCompares the counts of two groups
twoGroupsGOPerforms the GO analysis for two groups
vennFromSetsCreates a Venn diagram based on the overlapping elements in...
waitForFreeDiskSpaceChecks if there is enough free disk space
writeAnnotationFromGtfFeature annotation file operations
writeCountFilesToMetaWrite names of countfiles back into the input file
writeDEXSeqReportWriting a report for a DEXSeq analysis
writeErrorReportWrites an error report
writeIgvJnlpWrites a .jnlp file
writeIgvSessionWrites an IGV session
writeJavaScriptIgvStarterWrites a jnlp link to a static html
writeNgsMultiGroupReportWrites the report for the multi group analysis
writePresplicedGtfWrites pre-spliced annotation
writeSCMMRead and write single cell sparse matrix
zipFileArchives files
uzh/ezRun documentation built on Dec. 9, 2018, 1:20 p.m.