Man pages for HenrikBengtsson/aroma.seq
High-Throughput Sequence Analysis using the Aroma Framework
| AbstractAlignment | The AbstractAlignment class |
| AbstractIndexFile | The abstract AbstractIndexFile class |
| AbstractIndexSet | The AbstractIndexSet class |
| AromaSeq | The AromaSeq Package class |
| aroma.seq-package | Package aroma.seq |
| AromaSeqTransform | The AromaSeqTransform class |
| BamDataFile | The BamDataFile class |
| BamDataSet | The BamDataSet class |
| BamDownsampler | The BamDownsampler class |
| BamIndexDataFile | The abstract BamIndexDataFile class |
| BamMerger | The BamMerger class |
| BinnedGcNormalization | The abstract BinnedGcNormalization class |
| bowtie2 | Calls the Bowtie2 executable to align input reads |
| Bowtie2Alignment | The Bowtie2Alignment class |
| bowtie2Build | Creates index on reference genome using bowtie2-build |
| Bowtie2IndexFile | The abstract Bowtie2IndexFile class |
| Bowtie2IndexSet | The Bowtie2IndexSet class |
| buildBowtie2IndexSet.FastaReferenceFile | Builds a Bowtie2 index files set |
| buildBwaIndexSet.FastaReferenceFile | Builds a BWA index files set |
| buildDictionary.FastaReferenceFile | Builds a DICT sequence dictionary file |
| buildIndex.FastaReferenceFile | Builds an FAI index file |
| buildTopHat2TranscriptomeIndexSet.Bowtie2IndexSet | Calls TopHat to build a transcriptome index |
| BwaAlignment | The BwaAlignment class |
| bwaAln | BWA-backtrack alignment via 'bwa aln' |
| bwaIndex | Calls the BWA index command |
| BwaIndexFile | The abstract BwaIndexFile class |
| bwaIndexPrefix | Generates a prefix for the index files |
| BwaIndexSet | The BwaIndexSet class |
| bwaSampe | Generates BWA-backtrack paired-end (PE) alignments via 'bwa... |
| bwaSamse | Generates BWA-backtrack single-end (SE) alignments via 'bwa... |
| byOrganism.FastaReferenceFile | Locates a FASTA file by organism |
| byOrganism.GtfDataFile | Locates a GTF file by organism |
| capabilitiesOf.AromaSeq | Checks which tools are supported |
| convertToBam | Converts a SAM file (set of files) set into a (sorted and... |
| convertToSam | Converts a SAM (BAM) file (set of files) set into a BAM (SAM)... |
| createIndexPrefix | Generates a prefix for a set of index files |
| cuffdiff | Calls cuffdiff on input bam file(s) |
| cufflinks | Calls cufflinks on input bam file(s) |
| doBowtie2 | Read alignment using the Bowtie v2 aligner |
| doBWA | Read alignment using the Burrows-Wheeler Transform aligner... |
| doDownsample | Generates a downsampled FASTQ or BAM data set |
| doHTSeqCount | Counting reads in features |
| doQDNAseq | Quantitative inference of copy number aberrations with DNA... |
| doTopHat2 | Read alignment using the TopHat v2 aligner |
| FastaReferenceFile | The FastaReferenceFile class |
| FastaReferenceIndexFile | The FastaReferenceIndexFile class |
| FastaReferenceSet | The FastaReferenceSet class |
| fastQC | Calls the FastQC executable |
| FastQCDataFile | The abstract FastQCDataFile class |
| FastQCDataFileSet | The FastQCDataFileSet class |
| FastQCReporter | The FastQCReporter class |
| FastqDataFile | The abstract FastqDataFile class |
| FastqDataSet | The FastqDataSet class |
| FastqDownsampler | The FastqDownsampler class |
| fastqDump | Calls the fastq-dump executable |
| findCmd | Locates the executable given by 'command' |
| findCmdv | Locates the executable given by 'command'; tests version if... |
| findExternal | Locates an external executable |
| findFilesTodo | Identifies which files are not yet processed |
| gatk | Calls the GATK executable |
| getOutputDataSet | Gets the (complete or incomplete) processed output data set |
| GtfDataFile | The GtfDataFile class |
| htseqCount | Calls the htseq-count executable to count input reads on... |
| HTSeqCountDataFile | The HTSeqCountDataFile class |
| HTSeqCountDataSet | The HTSeqCountDataSet class |
| HTSeqCounting | The HTSeqCounting class |
| IlluminaFastqDataFile | The abstract IlluminaFastqDataFile class |
| IlluminaFastqDataSet | The IlluminaFastqDataSet class |
| Non-documented_objects | Non-documented objects |
| normalizeGcContent | Normalizes signals for GC-content effects |
| onExit | Records expressions to be executed when the current function... |
| PairedEndFastqDataSet | The PairedEndFastqDataSet class |
| PicardDuplicateRemoval | The PicardDuplicateRemoval class |
| process.Bowtie2Alignment | Runs the aligner |
| process.BwaAlignment | Runs the BWA aligner |
| QDNAseqEstimation | The QDNAseqEstimation class |
| readDGE.HTSeqCountDataSet | Reads all digital gene expression (DGE) data |
| readSeqFile | Reads and summarizes a FASTQ file |
| SamDataFile | The abstract SamDataFile class |
| SamDataSet | The SamDataSet class |
| SamReadGroup | The SamReadGroup class |
| samtoolsFaidx | Calls the samtools 'faidx' command |
| samtoolsMpileup | Calls the samtools 'mpileup' command |
| samtoolsSort | Calls the samtools 'sort' command |
| samtoolsView | Calls the samtools 'view' command |
| SamTransform | The SamTransform class |
| SequenceContigsInterface | The SequenceContigsInterface class |
| setupExampleData | Setups example data in the current directory |
| sortByName | Produce sorted and indexed BAM file(s) from BAM file(s); this... |
| sortByPosition | Produce sorted and indexed BAM file(s) from BAM file(s) |
| SraDataFile | The abstract SraDataFile class |
| SraDataSet | The SraDataSet class |
| systemBowtie2 | Wrapper for bowtie2 |
| systemBowtie2Build | Wrapper for bowtie2-build |
| systemBWA | Calls the BWA executable |
| systemCuffdiff | Calls the Cuffdiff executable to perform isoform abundance... |
| systemCufflinks | Calls the Cufflinks executable to perform isoform abundance... |
| systemFastQC | Calls the FastQC executable |
| systemFastqDump | Wrapper for fastq-dump SRA utility |
| systemGATK | Calls the GATK executable |
| systemGenericCmd | Wrapper to call 'command' using system2() |
| systemHTSeqCount | Wrapper for htseq-count |
| systemJava | Calls the Java executable |
| systemJavaJar | Calls the Java jar executable |
| systemPicard | Calls the Picard executable |
| systemSamtools | Calls the samtools executable |
| systemSraToolkit | Calls an SRA Toolkit executable |
| systemTopHat | Wrapper for tophat |
| systemTopHatBuild | Calls the TopHat executable, specifically to build a... |
| tophat | Calls the TopHat executable to align input reads |
| TopHat2Alignment | The TopHat2Alignment class |
| TotalCnBinnedCounting | The TotalCnBinnedCounting class |
| validate.BamDataFile | Validates a BAM (or SAM) file |
| writeFastaReferenceFile.FastaReferenceSet | Writes the content of multiple FASTA files into a new FASTA... |
