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GenomicTools.fileHandler (version 0.1.5.9)

File Handlers for Genomic Data Analysis

Description

A collection of I/O tools for handling the most commonly used genomic datafiles, like fasta/-q, bed, gff, gtf, ped/map and vcf.

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Install

install.packages('GenomicTools.fileHandler')

Monthly Downloads

361

Version

0.1.5.9

License

GPL (>= 2)

Maintainer

Daniel Fischer

Last Published

March 5th, 2020

Functions in GenomicTools.fileHandler (0.1.5.9)

exportBed

Exporting a Bed File.
example.fastq

Example Sequencing Reads in fastq-Format
example.fasta

Example Sequencing Reads in fasta-Format
example2.gtf.gz

Example Gene Annotation in zipped gtf-Format
example.gff

Example Gene Annotation in gff-Format
exportFA

Exporting a Fasta File.
importBed

Importing a Bed File.
example.gtf

Example Gene Annotation in gtf-Format
GenomicTools.fileHandler-package

R Package To Handle Files From Genomic Data GenomicTools.fileHandler is a loose collection of I/O Functions Needed in Genomic Data Analysis
example.bed

Example Gene Annotation in Bed-Format
example.ped

Example Variant data in ped/map-Format
importGTF

Import a GTF File
print.bed

Print a bed Object
importFA

Importing a Fasta File.
importBlastTab

Import a Tab Delimited Blast Output File
importPED

importPED
importGFF

importGFF
example.vcf

Example Variant data in vcf-Format
importGFF3

importGFF3
plotUniquelyMappedReads

plotUniquelyMappedReads
prereadGTF

prereadGTF
print.fa

Print a fa Object
print.vcf

Print a vcf Object
summary.gtf

Summary of a gtf Object
importFeatureCounts

Import from FeatureCounts
importFQ

Importing a Fastq File.
summary.STARLog

Summary of a STARLog Object
importSTARLog

importSTARLog
summary.fa

Summary of a fa Object
print.fq

Print a fq Object
importVCF

importVCF
summary.bed

Summary of a bed Object
print.featureCounts

Print a featureCounts Object
importXML

importXML
summary.featureCounts

Summary of a featureCounts Object
plotTotalReads

plotTotalReads
summary.fq

Summary of a fq Object
print.gtf

Print a gtf Object
print.pedMap

Print a pedMap Object