Man pages for uzh/ezRun
An R meta-package for the analysis of Next Generation Sequencing Data
| abundPlot | Rank-specific abundance plot |
| add_centered_title | Formats ggplot title |
| addCountResultSummary | Adds a summary of the count result |
| addDataset | Adds a dataset |
| addJavaScriptIgvStarter | Adds a java function |
| addQcScatterPlots | Adds QC scatter plots |
| addResultFile | Adds a result file |
| addTxtLinksToReport | Adds text links |
| annotatePeaks | Annotates peaks |
| averageColumns | Averages columns together |
| averageRows | Averages rows together |
| bam2bw | Bam to bigwig |
| bam2fastq | Bam/Sam file to fastq file conversion |
| calmdBam | Calculate MD tag for BAM |
| chimeraSummaryPlot | Chimera identification |
| chimeraSummaryTable | Chimera identification |
| cleanGenomeFiles | Cleans genome files |
| cleanupTwoGroupsInput | Cleans up input from two group apps |
| clusterHeatmap | Plots the cluster heatmap |
| CollectAlignmentSummaryMetrics | CollectAlignmentSummaryMetrics |
| CollectRnaSeqMetrics | CollectRnaSeqMetrics |
| colorClusterLabels | Gets the color cluster labels |
| communityPercSummTable | Summary of community composition |
| computeBamStats | Computes the BAM statistics |
| computeDnaBamStats | Computes the DnaQC statistics |
| computeRangeStats | Computes stats of genomic ranges |
| consensusPeaks | Get consensus peaks |
| convertGtfToGff | Convert annotation file from GTF format to GFF |
| convStepTable | Clustering steps |
| countAndAssignSeqsFromFasta | Mothur fasta summary |
| countDensPlot | Plots the count densities |
| countReadsInFastq | Counts reads in FastQ files |
| createSaturationTableForKableExtra | Creates saturation convergence table for Kable_extra output |
| createStepConvTableForKableExtra | Creates step convergence table for Kable_extra output |
| createSummaryTable | Mothur Summary Table |
| createSummaryTableForKableExtra | Merges summary tables for Kable_extra output |
| DADA2CreateSeqTab | Main DADA2 workflow (sample-wise) |
| DADA2mergeSeqTabs | DADA2 seqtab merging, removing chimeras and assigning... |
| datasetToMothur | Creates Mothur input files from Sushi dataset. |
| doGo | Do GO? |
| dupBam | Duplicates operation in bam |
| DuplicationMetrics | DuplicationMetrics |
| enrichrAddList | Add gene list |
| enrichrEnrich | Enrichment analysis |
| errorRateSummaryPlot | Error rate |
| expandGRanges | Expands genomic ranges |
| extractTopN | Prepares all the interproscan-associated files; the sceond... |
| ezAllPairScatter | Does scatter plots of all pairs |
| EzAppATACSeqQC-class | The R5 class representing a runnable app using... |
| EzAppBamPreview-class | The R5 class representing a runnable app using... |
| EzAppBismark-class | The R5 class representing a runnable app using... |
| EzAppBowtie2-class | The R5 class representing a runnable app using... |
| EzAppBowtie2Transcriptome-class | The R5 class representing a runnable app using... |
| EzAppBowtie-class | The R5 class representing a runnable app using... |
| EzAppBWA-class | The R5 class representing a runnable app using... |
| EzAppCanu-class | The R5 class representing a runnable app using... |
| EzAppCellRanger-class | The R5 class representing a runnable app using... |
| EzAppChipStats-class | The R5 class representing a runnable app using... |
| EzApp-class | The R5 class representing a runnable app |
| EzAppCNVnator-class | The R5 class representing a runnable app using... |
| EzAppCountOverlaps-class | The R5 class representing a runnable app using... |
| EzAppCountQC-class | The R5 class representing a runnable app using... |
| EzAppDADA2Step1Sample-class | The R5 class representing a runnable app using... |
| EzAppDADA2Step2Dataset-class | The R5 class representing a runnable app using... |
| EzAppDeseq2-class | The R5 class representing a runnable app using... |
| EzAppDEXSeqAnalysis-class | The R5 class representing a runnable app using... |
| EzAppDnaQC-class | The R5 class representing a runnable app using... |
| EzAppEdger-class | The R5 class representing a runnable app using... |
| EzAppENA-class | The R5 class representing a runnable app using... |
| EzAppFastqc-class | The R5 class representing a runnable app using... |
| EzAppFastqScreen-class | The R5 class representing a runnable app using... |
| EzAppFeatureCounts | FeatureCounts App |
| EzAppFeatureCounts-class | The R5 class representing a runnable app using... |
| EzAppFlash-class | The R5 class representing a runnable app using... |
| EzAppGatkDnaHaplotyper-class | The R5 class representing a runnable app using... |
| EzAppGatkRna-class | The R5 class representing a runnable app using... |
| EzAppHGAP-class | The R5 class representing a runnable app using... |
| EzAppJoinGenoTypes-class | The R5 class representing a runnable app using... |
| EzAppJunctionSeq-class | The R5 class representing a runnable app using... |
| EzAppKallisto-class | The R5 class representing a runnable app using... |
| EzAppKraken-class | The R5 class representing a runnable app using... |
| EzAppMacs2-class | The R5 class representing a runnable app using... |
| EzAppMegahit-class | The R5 class representing a runnable app using... |
| EzAppMEME-class | The R5 class representing a runnable app using... |
| EzAppMetagenomeAnnotationQC-class | The R5 class representing a runnable app using... |
| EzAppMetaquast-class | The R5 class representing a runnable app using... |
| EzAppMetaspades-class | The R5 class representing a runnable app using... |
| EzAppMothurStep1Sample-class | The R5 class representing a runnable app using... |
| EzAppMothurStep1SampleReport-class | The R5 class representing a runnable app using... |
| EzAppMothurStep2Dataset-class | The R5 class representing a runnable app using... |
| EzAppMothurStep2DatasetReport-class | The R5 class representing a runnable app using... |
| EzAppMpileup-class | The R5 class representing a runnable app using... |
| EzAppNcpro-class | The R5 class representing a runnable app using... |
| EzAppPhyloSeqAnalysis-class | The R5 class representing a runnable app using... |
| EzAppQuast-class | The R5 class representing a runnable app using... |
| EzAppResequencing-class | The R5 class representing a runnable app using... |
| EzAppRnaBamStats-class | The R5 class representing a runnable app using... |
| EzAppRSEM-class | The R5 class representing a runnable app using... |
| EzAppSalmon-class | The R5 class representing a runnable app using... |
| EzAppSCCounts-class | The R5 class representing a runnable app using... |
| EzAppSGSeq-class | The R5 class representing a runnable app using... |
| EzAppSpades-class | The R5 class representing a runnable app using... |
| EzAppSplitAndCluster-class | The R5 class representing a runnable app using... |
| EzAppSTAR-class | The R5 class representing a runnable app using... |
| EzAppSubreads-class | The R5 class representing a runnable app using... |
| EzAppTeqc-class | The R5 class representing a runnable app using... |
| EzAppTophat-class | The R5 class representing a runnable app using... |
| EzAppTranscriptCoverage-class | The R5 class representing a runnable app using... |
| EzAppTrinity-class | The R5 class representing a runnable app using... |
| EzAppUparse-class | The R5 class representing a runnable app using... |
| EzAppVirDetect-class | The R5 class representing a runnable app using... |
| ezBam2bigwig | Converts from bam to bigwig |
| ezBamSeqNames | Gets sequence names |
| ezBuildAttributeField | Builds an annotation attributes field |
| ezChromSizesFromVcf | Gets chromosome sizes from a VCF file |
| ezCollapse | Collapses a vector in a single character |
| ezColorLegend | Plots a color scale |
| ezColorLegendGG2 | Plots a color scale with ggplot2 |
| ezCombineReadDatasets | Combine the reads from multiple datasets into a single... |
| ezComputeBias | compute and plot the GC content and gene-length associated... |
| ezCorrelationPlot | Does a correlation plot |
| ezCut | Convert numeric to factor |
| EzDataset-class | The R5 class representing a dataset |
| ezDesignFromDataset | Gets the design from the dataset |
| ezDuplicated | Which values are duplicated? |
| ezFilterVcf | Filters a VCF file and writes it back |
| ezFlexTable | Wrapper for 'FlexTable()' |
| ezFrame | Wrapper for data.frame suitable for data processing rather... |
| ezGeomean | Geometric mean |
| ezGrepl | Matches patterns and returns a logical vector |
| ezGroupGO | Groups GO terms and information |
| ezHead | Writes the head of a file |
| ezHeatmap | Plots a heatmap |
| ezImageFileLink | Gets an image link as html |
| ezInteractiveTable | Saves an interactive table |
| ezInteractiveTableRmd | Generates an interactive table |
| ezIntString | Format an integer into a character using only digits |
| ezIsAbsolutePath | Is x an absolute file path? |
| ezIsSpecified | Check if a value is specified |
| ezJobStart | Writes start time of job |
| ezLegend | Plots a legend |
| ezLoadFeatures | Loads annotation features from a file |
| ezLogmeanNorm | Scales columns of a matrix to logarithmic mean |
| ezMail | Mails information, the nodename and working directory |
| ezMatrix | Creates a matrix |
| ezMclapply | Parallel version of 'lapply()' |
| ezMdsPlot | Plots the multi dimensional scaling |
| ezMedianNorm | Scales columns of a matrix to median |
| ezMethodDEXSeqAnalysis | RunMethod for reference class EzAppDEXSeqAnalysis |
| ezMethodSubsampleReads | Subsample reads in a fastq dataset file |
| ezMethodTrim | Trims input reads |
| ezMultiplicated | Which values occur at least 'n' times? |
| ezNorm | Normalization |
| ezParam | Build parameter object |
| ezPresentFlags | Which values to keep? |
| ezQuantileNorm | Quantile Normalization |
| ezReadGappedAlignments | Reads gapped alignments from bam |
| ezReadGff | Reads an annotation table from a file. |
| ezReadPairedAlignments | Reads paired alignments from bam |
| ezRead.table | Modified version of read.table |
| EzRef-class | The S4 class representing a collection of information about... |
| ezReplicateNumber | Count how often a value has been seen before |
| EzResult-class | The object that represents a result of an expression analysis |
| ezRun-package | a meta-package that integrates NGS related R-packages and... |
| ezScaleColumns | Scales columns of a matrix |
| ezScanBam | Scans a bam file |
| ezScatter | Does scatter plots |
| ezSessionInfo | Saves session info in a .txt file |
| ezSmoothScatter | Does smooth scatter plots |
| ezSortIndexBam | Sorts and indexes a bam file |
| ezSplit | Separates a character vector into a matrix by splitting it. |
| ezSplitLongLabels | Splits long labels into two lines |
| ezSystem | Invokes a system command |
| ezThreads | Determines the number of CPU cores to be used |
| ezTime | Modified version of Sys.time() |
| ezTranscriptDbFromRef | Gets the transcripts database from the reference |
| ezUtrSequences | Gets UTR sequences |
| ezValidFilename | Enforces a valid file name |
| ezValidMail | Is the email-address valid? |
| ezVolcano | Volcano plot |
| ezVsnNorm | Variance Stabilizing Normalization |
| ezWrite | Write in a single line |
| ezWriteElapsed | Writes elapsed time of job |
| ezWrite.table | Modified version of write.table |
| ezXYScatter.2 | XYScatter plot |
| fastqs2bam | Fastq files to Bam with RG tag |
| featAnnoIO | Feature annotation file IO |
| filterEnrichrResults | Result filtering |
| filterFastqByBam | Filters FastQ files by bam |
| filteroutBam | Filter bam |
| fixStrand | Fixes the strand information |
| generateFlattenedFileForSGeq | Generate flattened file for SGSeq-based differential... |
| getBamMultiMatching | Gets bam multi matching |
| getBlacklistedRegions | Get blacklisted genomic regions |
| getBlueRedScale | Gets a color scale from blue to red |
| getBowtie2Reference | Builds and gets a Bowtie2 reference |
| getBowtie2TranscriptomeReference | Builds and gets a Bowtie2 reference |
| getBowtieReference | Builds and gets a Bowtie reference |
| getBWAReference | Builds and gets a BWA reference |
| getCellRangerGEXReference | Build CellRanger index |
| getDupRateFromBam | Duplication rate from Bam of RNA-Seq. |
| getEnrichrLibNames | Get Enrichr library names |
| getEnsemblTypes | Gets the ensembl types |
| getExonNumber | Gets the exon numbers |
| getGeneIdExprLinks | Get Links from GeneIds to Expression result files |
| getGeneMapping | Gets the isoform-to-gene mapping |
| getGeneTable | Generate gene table from DEXSeqResults object |
| getGOparents | Gets the GO parents |
| getIgvLocusLink | Gets an IGV locus link in .html format |
| getKallistoReference | Builds and gets a kallisto reference |
| getQualityMatrix | Get quality matrix |
| getRangeValues | Gets the values of genomic ranges |
| getReferenceFeaturesBed | Gets a bed file |
| getRpkm | Get measurements from rawData |
| getRSEMReference | Builds and gets a RSEM reference |
| getSalmonReference | Builds and gets a salmon reference |
| getSampleColors | Gets the sample colors |
| getSTARReference | Builds and gets a STAR reference |
| getSuffix | Gets the suffix of a file name |
| getTranscript2Gene | Gets gene names from annotation |
| getTranscriptCoverage | Gets transcripts coverage |
| getTranscriptGcAndWidth | Gets GC proportions and gene widths |
| getTranscriptSequences | Gets transcript sequences |
| getTuxedoLibraryType | Gets the tuxedo library type |
| gffToRanges | Gets GRanges from annotation |
| gffTrimTranscripts | Trims transcripts in annotation data.frames |
| gffUtilities | gff utilities functions |
| goClusterTableRmd | Gets the GO cluster table |
| goStringsToList | Parses GO strings to a list |
| groupGff | Groups annotation |
| groupModRichPlot | Modified phyloseq richness plot |
| hasFilesafeCharacters | Checks if the argument can be safely used as a filename |
| heatmapForPhylotseqPlotPheatmap | Alternative heatmap with pheatmap plot for phyloseq... |
| imgLinks | Pastes image links as html |
| import.Macs2Peaks | Import the MACS2 peak file |
| interleaveMatricesByColumn | Combines two matrices by their columns |
| intHist | Shrinks values and plots a histogram |
| inverseMapping | Inverse mapping |
| isError | Tests if x contains an error |
| isValidCigar | Is 'x' a valid cigar? |
| lastVal | Gets the last value of an object |
| lGetGlobalCountParam | specification of default values used for count splitting |
| loadCountDataset | Loads the count dataset |
| loadSCCountDataset | Loads the count dataset of single cell experiment |
| logMessage | Logs time and base directory together with a parameter |
| makeCoordinate | Make a coordinate |
| makeExtraControlSeqGR | Functions for control sequences |
| makeMinimalSingleEndReadDataset | Makes a minimal single end dataset |
| makeSGSeqtxdbObject | Create and save SGSea database |
| mioString | Converts a number into a character representing millions |
| mixedDatasetToMothur | Creates Mothur input files from Sushi dataset. |
| mkCurlQryString | Query string generator |
| modifyInput | input is modified to show the count results |
| ncpro | Analysis of small RNA sequences using ncpro |
| openBsdocReport | Opens an html report |
| ordPlot | Rank-specific tax-based ordination plot |
| otuSaturationTable | OTUs saturation table |
| parseEnrichrLibNames | Retrieve Enrichr library names |
| pcaForPhyloseqPlot | Alternative pca plot for phyloseq abundnce-taxonimy matrix |
| phyloSeqCommunityComp | Rank summary plots |
| phyloSeqDivPlotAndPercUnclassified | Richness plot for a certain taxa |
| phyloSeqOTU | Phyloseq OTU object |
| phyloSeqOTUFromFile | Phyloseq OTU object |
| phyloSeqPreprocess | Phyloseq preprocess |
| phyloSeqSample | Phyloseq Sample object |
| phyloSeqTaxa | Phyloseq Taxa object |
| phyloSeqTaxaFromFile | Phyloseq Taxa object |
| phyloSeqToDeseq2_tableAndPlots | Differential abundance analysis between groups |
| plateStatistics | Bias inspection per plate |
| plotBarMod | modified phyloseq barplot |
| plotLocusCoverageProfile | Title |
| postProcessResults | Postprocessing counts produced as results from ncpro |
| prodigalFileReport | Prepares all the prodigal-associated files |
| rarefactionPlot | OTUs saturation plot |
| readNcProResult | Reads NcPro results |
| runCountSingleBam | Run counts for a single BAM file |
| runEnrichr | Run Enrichr |
| runTEQC | Runs the target enrichment quality control |
| selectFeatures | Selects features from raw data |
| separateGoIdsByOnto | Separates GO ID's by ontology |
| setwdNew | Switches to a working directory |
| shiftZeros | Shifts zeros |
| shrinkToRange | Shrink the dynamic range of a numeric vector, matrix, or data... |
| splitBamByRG | Split bam file |
| splitCoordinate | Splits fragment coordinates |
| splitCounts | split count result into different files and put them into... |
| strandValue | Gets a strand value |
| subSampleRle | Subsets an Rle object |
| subsetRankTopN | Select only top10 rank |
| subsetTaxMod | Modifed subset taxa |
| summaryMatchScorePlot | Prepares all the IPS-associated plots |
| summaryScorePlot | Prepares all the prodigal-associated plots |
| tableFromSets | Creates a contingency table from a list of vectors. |
| trimGRanges | trim GRanges object |
| trimWhiteSpace | Trims white space |
| twoGroupCountComparison | Compares the counts of two groups |
| twoGroupsGO | Performs the GO analysis for two groups |
| vennFromSets | Creates a Venn diagram based on the overlapping elements in... |
| waitForFreeDiskSpace | Checks if there is enough free disk space |
| writeAnnotationFromGtf | Feature annotation file operations |
| writeCountFilesToMeta | Write names of countfiles back into the input file |
| writeDEXSeqReport | Writing a report for a DEXSeq analysis |
| writeErrorReport | Writes an error report |
| writeIgvJnlp | Writes a .jnlp file |
| writeIgvSession | Writes a jnlp link to a static html |
| writeOTUgzFileForVamps | OTUs saturation table conversion for VAMPs |
| writePresplicedGtf | Writes pre-spliced annotation |
| writeSCMM | Read and write single cell sparse matrix |
| zipFile | Archives files |
