Package: GenomicTools.fileHandler 0.2.2

GenomicTools.fileHandler: File Handlers for Genomic Data Analysis

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

Authors:Daniel Fischer

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GenomicTools.fileHandler.pdf |GenomicTools.fileHandler.html✨
GenomicTools.fileHandler/json (API)

# Install 'GenomicTools.fileHandler' in R:
install.packages('GenomicTools.fileHandler', repos = c('https://fischuu.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/fischuu/genomictools.filehandler/issues

On CRAN:

4.48 score 2 packages 4 scripts 359 downloads 5 mentions 17 exports 8 dependencies

Last updated 11 months agofrom:bb07eed5c1. Checks:1 OK, 6 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 23 2025
R-4.5-winWARNINGJan 23 2025
R-4.5-linuxWARNINGJan 23 2025
R-4.4-winWARNINGJan 23 2025
R-4.4-macWARNINGJan 23 2025
R-4.3-winWARNINGDec 24 2024
R-4.3-macWARNINGDec 24 2024

Exports:exportBedexportFAexportGTFimportBedimportBlastTabimportFAimportFeatureCountsimportFQimportGFFimportGFF3importGTFimportPEDimportSTARLogimportVCFimportXMLplotTotalReadsplotUniquelyMappedReads

Dependencies:BiocGenericsdata.tablegenericslatticeMatrixsnpStatssurvivalzlibbioc

An Introduction to GenomicTools.fileHandler

Daniel Fischer

Rendered fromGenomicTools.fileHandler-Vignette.Rmdusingknitr::rmarkdownon Jan 23 2025.

Last update: 2018-07-26
Started: 2018-07-26

Readme and manuals

Help Manual

Help pageTopics
R Package To Handle Files From Genomic Data GenomicTools.fileHandler is a loose collection of I/O Functions Needed in Genomic Data AnalysisGenomicTools.fileHandler-package
Example Gene Annotation in Bed-Formatexample.bed
Example Sequencing Reads in fasta-Formatexample.fasta
Example Sequencing Reads in fastq-Formatexample.fastq
Example Gene Annotation in gff-Formatexample.gff
Example Gene Annotation in gtf-Formatexample.gtf
Example Variant data in ped/map-Formatexample.ped
Example Variant data in vcf-Formatexample.vcf
Example Gene Annotation in zipped gtf-Formatexample2.gtf.gz
Exporting a Bed File.exportBed
Exporting a Fasta File.exportFA
Exporting a GTF File.exportGTF
Importing a Bed File.importBed
Import a Tab Delimited Blast Output FileimportBlastTab
Importing a Fasta File.importFA
Import from FeatureCountsimportFeatureCounts
Importing a Fastq File.importFQ
importGFFimportGFF
importGFF3importGFF3
Import a GTF FileimportGTF
importPEDimportPED
importSTARLogimportSTARLog
importVCFimportVCF
importXMLimportXML
plotTotalReadsplotTotalReads
plotUniquelyMappedReadsplotUniquelyMappedReads
prereadGTFprereadGTF
Print a bed Objectprint.bed
Print a fa Objectprint.fa
Print a featureCounts Objectprint.featureCounts
Print a fq Objectprint.fq
Print a gtf Objectprint.gtf
Print a pedMap Objectprint.pedMap
Print a vcf Objectprint.vcf
Summary of a bed Objectsummary.bed
Summary of a fa Objectsummary.fa
Summary of a featureCounts Objectsummary.featureCounts
Summary of a fq Objectsummary.fq
Summary of a gtf Objectsummary.gtf
Summary of a STARLog Objectsummary.STARLog