RNAprobR: An R package for analysis of massive parallel sequencing based RNA structure probing data

This package facilitates analysis of Next Generation Sequencing data for which positional information with a single nucleotide resolution is a key. It allows for applying different types of relevant normalizations, data visualization and export in a table or UCSC compatible bedgraph file.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RNAprobR")
AuthorLukasz Jan Kielpinski [aut], Nikos Sidiropoulos [cre, aut], Jeppe Vinther [aut]
Bioconductor views Coverage GenomeAnnotation Normalization Sequencing
Date of publicationNone
MaintainerNikos Sidiropoulos <nikos.sidiro@gmail.com>
LicenseGPL (>=2)
Version1.8.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/auxiliary_functions.R R/bam2bedgraph.R R/bed_to_TranscriptDb.R R/bedgraph2norm.R R/comp.R R/compdata.R R/correct_oversaturation.R R/dtcr.R R/finishing.R R/k2n_calc.R R/norm2bedgraph.R R/readsamples.R R/slograt.R R/swinsor.R
RNAprobR.Rproj
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/RNAprobR.R
inst/doc/RNAprobR.Rnw
inst/doc/RNAprobR.pdf
inst/extdata
inst/extdata/RNaseP.bed
inst/extdata/hrfseq.fa
inst/extdata/hrfseq.fa.fai
inst/extdata/k2n_14
inst/extdata/k2n_16
inst/extdata/k2n_22
inst/extdata/k2n_24
inst/extdata/unique_barcodes14.gz
inst/extdata/unique_barcodes16.gz
inst/extdata/unique_barcodes22.gz
inst/extdata/unique_barcodes24.gz
man
man/BED2txDb.Rd man/GR2norm_df.Rd man/bam2bedgraph.Rd man/bedgraph2norm.Rd man/comp.Rd man/compdata.Rd man/correct_oversaturation.Rd man/dtcr.Rd man/k2n_calc.Rd man/norm2bedgraph.Rd man/norm_df2GR.Rd man/plotRNA.Rd man/plotReads.Rd man/readsamples.Rd man/slograt.Rd man/swinsor.Rd man/swinsor_vector.Rd man/winsor.Rd
vignettes
vignettes/RNAprobR.Rnw
vignettes/refs.bib
vignettes/workflow.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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