Man pages for HenrikBengtsson/aroma.seq
High-Throughput Sequence Analysis using the Aroma Framework

AbstractAlignmentThe AbstractAlignment class
AbstractIndexFileThe abstract AbstractIndexFile class
AbstractIndexSetThe AbstractIndexSet class
AromaSeqThe AromaSeq Package class
aroma.seq-packagePackage aroma.seq
AromaSeqTransformThe AromaSeqTransform class
BamDataFileThe BamDataFile class
BamDataSetThe BamDataSet class
BamDownsamplerThe BamDownsampler class
BamIndexDataFileThe abstract BamIndexDataFile class
BamMergerThe BamMerger class
BinnedGcNormalizationThe abstract BinnedGcNormalization class
bowtie2Calls the Bowtie2 executable to align input reads
Bowtie2AlignmentThe Bowtie2Alignment class
bowtie2BuildCreates index on reference genome using bowtie2-build
Bowtie2IndexFileThe abstract Bowtie2IndexFile class
Bowtie2IndexSetThe Bowtie2IndexSet class
buildBowtie2IndexSet.FastaReferenceFileBuilds a Bowtie2 index files set
buildBwaIndexSet.FastaReferenceFileBuilds a BWA index files set
buildDictionary.FastaReferenceFileBuilds a DICT sequence dictionary file
buildIndex.FastaReferenceFileBuilds an FAI index file
buildTopHat2TranscriptomeIndexSet.Bowtie2IndexSetCalls TopHat to build a transcriptome index
BwaAlignmentThe BwaAlignment class
bwaAlnBWA-backtrack alignment via 'bwa aln'
bwaIndexCalls the BWA index command
BwaIndexFileThe abstract BwaIndexFile class
bwaIndexPrefixGenerates a prefix for the index files
BwaIndexSetThe BwaIndexSet class
bwaSampeGenerates BWA-backtrack paired-end (PE) alignments via 'bwa...
bwaSamseGenerates BWA-backtrack single-end (SE) alignments via 'bwa...
byOrganism.FastaReferenceFileLocates a FASTA file by organism
byOrganism.GtfDataFileLocates a GTF file by organism
capabilitiesOf.AromaSeqChecks which tools are supported
convertToBamConverts a SAM file (set of files) set into a (sorted and...
convertToSamConverts a SAM (BAM) file (set of files) set into a BAM (SAM)...
createIndexPrefixGenerates a prefix for a set of index files
cuffdiffCalls cuffdiff on input bam file(s)
cufflinksCalls cufflinks on input bam file(s)
doBowtie2Read alignment using the Bowtie v2 aligner
doBWARead alignment using the Burrows-Wheeler Transform aligner...
doDownsampleGenerates a downsampled FASTQ or BAM data set
doHTSeqCountCounting reads in features
doQDNAseqQuantitative inference of copy number aberrations with DNA...
doTopHat2Read alignment using the TopHat v2 aligner
FastaReferenceFileThe FastaReferenceFile class
FastaReferenceIndexFileThe FastaReferenceIndexFile class
FastaReferenceSetThe FastaReferenceSet class
fastQCCalls the FastQC executable
FastQCDataFileThe abstract FastQCDataFile class
FastQCDataFileSetThe FastQCDataFileSet class
FastQCReporterThe FastQCReporter class
FastqDataFileThe abstract FastqDataFile class
FastqDataSetThe FastqDataSet class
FastqDownsamplerThe FastqDownsampler class
fastqDumpCalls the fastq-dump executable
findCmdLocates the executable given by 'command'
findCmdvLocates the executable given by 'command'; tests version if...
findExternalLocates an external executable
findFilesTodoIdentifies which files are not yet processed
gatkCalls the GATK executable
getOutputDataSetGets the (complete or incomplete) processed output data set
GtfDataFileThe GtfDataFile class
htseqCountCalls the htseq-count executable to count input reads on...
HTSeqCountDataFileThe HTSeqCountDataFile class
HTSeqCountDataSetThe HTSeqCountDataSet class
HTSeqCountingThe HTSeqCounting class
IlluminaFastqDataFileThe abstract IlluminaFastqDataFile class
IlluminaFastqDataSetThe IlluminaFastqDataSet class
Non-documented_objectsNon-documented objects
normalizeGcContentNormalizes signals for GC-content effects
onExitRecords expressions to be executed when the current function...
PairedEndFastqDataSetThe PairedEndFastqDataSet class
PicardDuplicateRemovalThe PicardDuplicateRemoval class
process.Bowtie2AlignmentRuns the aligner
process.BwaAlignmentRuns the BWA aligner
QDNAseqEstimationThe QDNAseqEstimation class
readDGE.HTSeqCountDataSetReads all digital gene expression (DGE) data
readSeqFileReads and summarizes a FASTQ file
SamDataFileThe abstract SamDataFile class
SamDataSetThe SamDataSet class
SamReadGroupThe SamReadGroup class
samtoolsFaidxCalls the samtools 'faidx' command
samtoolsMpileupCalls the samtools 'mpileup' command
samtoolsSortCalls the samtools 'sort' command
samtoolsViewCalls the samtools 'view' command
SamTransformThe SamTransform class
SequenceContigsInterfaceThe SequenceContigsInterface class
setupExampleDataSetups example data in the current directory
sortByNameProduce sorted and indexed BAM file(s) from BAM file(s); this...
sortByPositionProduce sorted and indexed BAM file(s) from BAM file(s)
SraDataFileThe abstract SraDataFile class
SraDataSetThe SraDataSet class
systemBowtie2Wrapper for bowtie2
systemBowtie2BuildWrapper for bowtie2-build
systemBWACalls the BWA executable
systemCuffdiffCalls the Cuffdiff executable to perform isoform abundance...
systemCufflinksCalls the Cufflinks executable to perform isoform abundance...
systemFastQCCalls the FastQC executable
systemFastqDumpWrapper for fastq-dump SRA utility
systemGATKCalls the GATK executable
systemGenericCmdWrapper to call 'command' using system2()
systemHTSeqCountWrapper for htseq-count
systemJavaCalls the Java executable
systemJavaJarCalls the Java jar executable
systemPicardCalls the Picard executable
systemSamtoolsCalls the samtools executable
systemSraToolkitCalls an SRA Toolkit executable
systemTopHatWrapper for tophat
systemTopHatBuildCalls the TopHat executable, specifically to build a...
tophatCalls the TopHat executable to align input reads
TopHat2AlignmentThe TopHat2Alignment class
TotalCnBinnedCountingThe TotalCnBinnedCounting class
validate.BamDataFileValidates a BAM (or SAM) file
writeFastaReferenceFile.FastaReferenceSetWrites the content of multiple FASTA files into a new FASTA...
HenrikBengtsson/aroma.seq documentation built on Dec. 4, 2019, 11:27 p.m.