Package: TransView 1.51.0

Julius Muller

TransView: Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

This package provides efficient tools to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.

Authors:Julius Muller

TransView_1.51.0.tar.gz
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TransView.pdf |TransView.html✨
TransView/json (API)
NEWS

# Install 'TransView' in R:

install.packages('TransView', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

curl– Easy-to-use client-side URL transfer library
bzip2– High-quality block-sorting file compressor library
xz-utils– XZ-format compression library
zlib– Compression library

On BioConductor:TransView-1.51.0(bioc 3.21)TransView-1.50.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology dnamethylation geneexpression transcription microarray sequencing chipseq rnaseq methylseq dataimport visualization clustering multiplecomparison curl bzip2 xz-utils zlib

2.48 score 253 downloads 49 exports 24 dependencies

Last updated 10 days agofrom:4ecba1ba8d. Checks:ERROR: 2 WARNING: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Dec 17 2024
R-4.5-win-x86_64	WARNING	Oct 31 2024
R-4.5-linux-x86_64	ERROR	Oct 31 2024
R-4.4-win-x86_64	WARNING	Dec 17 2024
R-4.4-mac-x86_64	WARNING	Dec 17 2024
R-4.4-mac-aarch64	WARNING	Dec 17 2024
R-4.3-win-x86_64	WARNING	Dec 17 2024
R-4.3-mac-x86_64	WARNING	Dec 17 2024
R-4.3-mac-aarch64	WARNING	Dec 17 2024

Exports:annotatePeaks chromosomes cluster_order clusters collapsed compression data_pointer env ex_name ex_name<-filtered filtered_reads fmapmass gcoverage gsize gtf2gr histogram lcoverage lmaxScore lowqual lsize macs2gr maxScore meltPeak neg nreads origin paired paired_reads parameters parseReads peak2tss plotTV plotTVData pos proper_pairs readthrough_pairs rmTV show size slice1 slice1T sliceN sliceNT spliced spliced<-strands summaryTV tvStats

Dependencies:askpass BiocGenerics bitops caTools curl generics GenomeInfoDb GenomeInfoDbData GenomicRanges gplots gtools httr IRanges jsonlite KernSmooth mime openssl R6 Rhtslib S4Vectors sys UCSC.utils XVector zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets.	TransView-package TransView
Associates peaks to TSS	annotatePeaks
Class '"DensityContainer"'	chromosomes chromosomes,DensityContainer-method class:DensityContainer collapsed collapsed,DensityContainer-method compression compression,DensityContainer-method data_pointer data_pointer,DensityContainer-method DensityContainer-class env env,DensityContainer-method ex_name ex_name,DensityContainer-method ex_name<- ex_name<-,DensityContainer-method filtered filtered,DensityContainer-method filtered_reads filtered_reads,DensityContainer-method fmapmass fmapmass,DensityContainer-method gcoverage gcoverage,DensityContainer-method gsize gsize,DensityContainer-method lcoverage lcoverage,DensityContainer-method lmaxScore lmaxScore,DensityContainer-method lowqual lowqual,DensityContainer-method lsize lsize,DensityContainer-method maxScore maxScore,DensityContainer-method neg neg,DensityContainer-method nreads nreads,DensityContainer-method origin origin,DensityContainer-method paired paired,DensityContainer-method paired_reads paired_reads,DensityContainer-method pos pos,DensityContainer-method proper_pairs proper_pairs,DensityContainer-method readthrough_pairs readthrough_pairs,DensityContainer-method show,DensityContainer-method size size,DensityContainer-method spliced spliced,DensityContainer-method spliced<- spliced<-,DensityContainer-method strands strands,DensityContainer-method
GTF file parsing	gtf2gr
Histogram of the read distribution	histogram histogram,DensityContainer-method histogram-methods
Convenience function for MACS output conversion	macs2gr
Convenience function which returns a data frame with normalized peak densities suitable for plotting with ggplot2	meltPeak
User configurable efficient assembly of read density maps	parseReads
Changes the peak center to the next TSS according to previous annotation	peak2tss
Plot and cluster global read densities	plotTV
Summarize plotTV results	plotTVData plotTVData,TVResults plotTVData,TVResults-method plotTVData-methods
Free space occupied by DensityContainer	rmTV rmTV,DensityContainer-method rmTV-methods
Slice read densities from a TransView dataset	slice1 slice1,DensityContainer,character,numeric,numeric-method slice1-methods sliceN sliceN,DensityContainer-method sliceN-methods
Slice read densities of whole transcripts from a TransView DensityContainer	slice1T slice1T,DensityContainer,character-method slice1T-methods sliceNT sliceNT,DensityContainer,character-method sliceNT-methods
Class '"TVResults"'	class:TVResults clusters clusters,TVResults-method cluster_order cluster_order,TVResults-method parameters parameters,TVResults-method scores_peaks scores_peaks,TVResults-method scores_rna scores_rna,TVResults-method show,TVResults-method summaryTV summaryTV,TVResults-method TVResults-class
DensityContainer accessor function	tvStats tvStats,DensityContainer-method tvStats-methods