Package: GenomicTools.fileHandler 0.2.4

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

GenomicTools.fileHandler_0.2.4.tar.gz
GenomicTools.fileHandler_0.2.4.zip(r-4.7)GenomicTools.fileHandler_0.2.4.zip(r-4.6)GenomicTools.fileHandler_0.2.4.zip(r-4.5)
GenomicTools.fileHandler_0.2.4.tgz(r-4.6-any)GenomicTools.fileHandler_0.2.4.tgz(r-4.5-any)
GenomicTools.fileHandler_0.2.4.tar.gz(r-4.7-any)GenomicTools.fileHandler_0.2.4.tar.gz(r-4.6-any)
GenomicTools.fileHandler_0.2.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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'))

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

On CRAN:

4.18 score 1 packages 5 scripts 272 downloads 5 mentions 18 exports 7 dependencies

Last updated from:bc3f12be1b. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	133
source / vignettes	OK	344
linux-release-x86_64	ERROR	173
macos-release-arm64	ERROR	118
macos-oldrel-arm64	ERROR	104
windows-devel	ERROR	103
windows-release	ERROR	86
windows-oldrel	ERROR	91
wasm-release	OK	99

Exports:exportBed exportFA exportGTF exportVCF importBed importBlastTab importFA importFeatureCounts importFQ importGFF importGFF3 importGTF importPED importSTARLog importVCF importXML plotTotalReads plotUniquelyMappedReads

Dependencies:BiocGenerics data.table generics lattice Matrix snpStats survival

An Introduction to GenomicTools.fileHandler

Introduction

Rendered fromGenomicTools.fileHandler-Vignette.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

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