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{ "page": "GenomicTools.fileHandler-package", "title": "R Package To Handle Files From Genomic Data GenomicTools.fileHandler is a loose collection of I/O Functions Needed in Genomic Data Analysis", "topics": [ "GenomicTools.fileHandler-package" ] }, { "page": "example.bed", "title": "Example Gene Annotation in Bed-Format", "topics": [ "example.bed" ] }, { "page": "example.fasta", "title": "Example Sequencing Reads in fasta-Format", "topics": [ "example.fasta" ] }, { "page": "example.fastq", "title": "Example Sequencing Reads in fastq-Format", "topics": [ "example.fastq" ] }, { "page": "example.gff", "title": "Example Gene Annotation in gff-Format", "topics": [ "example.gff" ] }, { "page": "example.gtf", "title": "Example Gene Annotation in gtf-Format", "topics": [ "example.gtf" ] }, { "page": "example.ped", "title": "Example Variant data in ped/map-Format", "topics": [ "example.ped" ] }, { "page": "example.vcf", "title": "Example Variant data in vcf-Format", "topics": [ "example.vcf" ] }, { "page": "example2.gtf.gz", "title": "Example Gene Annotation in zipped gtf-Format", "topics": [ "example2.gtf.gz" ] }, { "page": "exportBed", "title": "Exporting a Bed File.", "topics": [ "exportBed" ] }, { "page": "exportFA", "title": "Exporting a Fasta File.", "topics": [ "exportFA" ] }, { "page": "exportGTF", "title": "Exporting a GTF File.", "topics": [ "exportGTF" ] }, { "page": "exportVCF", "title": "Exporting a VCF object.", "topics": [ "exportVCF" ] }, { "page": "importBed", "title": "Importing a Bed File.", "topics": [ "importBed" ] }, { "page": "importBlastTab", "title": "Import a Tab Delimited Blast Output File", "topics": [ "importBlastTab" ] }, { "page": "importFA", "title": "Importing a Fasta File.", "topics": [ "importFA" ] }, { "page": "importFeatureCounts", "title": "Import from FeatureCounts", "topics": [ "importFeatureCounts" ] }, { "page": "importFQ", "title": "Importing a Fastq File.", "topics": [ "importFQ" ] }, { "page": "importGFF", "title": "importGFF", "topics": [ "importGFF" ] }, { "page": "importGFF3", "title": "importGFF3", "topics": [ "importGFF3" ] }, { "page": "importGTF", "title": "Import a GTF File", "topics": [ "importGTF" ] }, { "page": "importPED", "title": "importPED", "topics": [ "importPED" ] }, { "page": "importSTARLog", "title": "importSTARLog", "topics": [ "importSTARLog" ] }, { "page": "importVCF", "title": "importVCF", "topics": [ "importVCF" ] }, { "page": "importXML", "title": "importXML", "topics": [ "importXML" ] }, { "page": "plotTotalReads", "title": "plotTotalReads", "topics": [ "plotTotalReads" ] }, { "page": "plotUniquelyMappedReads", "title": "plotUniquelyMappedReads", "topics": [ "plotUniquelyMappedReads" ] }, { "page": "prereadGTF", "title": "prereadGTF", "topics": [ "prereadGTF" ] }, { "page": "print.bed", "title": "Print a bed Object", "topics": [ "print.bed" ] }, { "page": "print.fa", "title": "Print a fa Object", "topics": [ "print.fa" ] }, { "page": "print.featureCounts", "title": "Print a featureCounts Object", "topics": [ "print.featureCounts" ] }, { "page": "print.fq", "title": "Print a fq Object", "topics": [ "print.fq" ] }, { "page": "print.gtf", "title": "Print a gtf Object", "topics": [ "print.gtf" ] }, { "page": "print.pedMap", "title": "Print a pedMap Object", "topics": [ "print.pedMap" ] }, { "page": "print.vcf", "title": "Print a vcf Object", "topics": [ "print.vcf" ] }, { "page": "summary.bed", "title": "Summary of a bed Object", "topics": [ "summary.bed" ] }, { "page": "summary.fa", "title": "Summary of a fa Object", "topics": [ "summary.fa" ] }, { "page": "summary.featureCounts", "title": "Summary of a featureCounts Object", "topics": [ "summary.featureCounts" ] }, { "page": "summary.fq", "title": "Summary of a fq Object", "topics": [ "summary.fq" ] }, { "page": "summary.gtf", "title": "Summary of a gtf Object", "topics": [ "summary.gtf" ] }, { "page": "summary.STARLog", "title": "Summary of a STARLog Object", "topics": [ "summary.STARLog" ] } ], 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