Package: NOISeq 2.57.0

Sonia Tarazona

NOISeq: Exploratory analysis and differential expression for RNA-seq data

Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions.

Authors:Sonia Tarazona, Pedro Furio-Tari, Maria Jose Nueda, Alberto Ferrer and Ana Conesa

NOISeq_2.57.0.tar.gz
NOISeq_2.57.0.zip(r-4.7)NOISeq_2.57.0.zip(r-4.6)NOISeq_2.57.0.zip(r-4.5)
NOISeq_2.57.0.tgz(r-4.6-any)NOISeq_2.57.0.tgz(r-4.5-any)
NOISeq_2.57.0.tar.gz(r-4.7-any)NOISeq_2.57.0.tar.gz(r-4.6-any)
NOISeq_2.57.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
NOISeq/json (API)

# Install 'NOISeq' in R:

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

Datasets:

mybiotypes - Marioni's dataset
mychroms - Marioni's dataset
mycounts - Marioni's dataset
mydata - Example of objects used and created by the NOISeq package
myfactors - Marioni's dataset
mygc - Marioni's dataset
mylength - Marioni's dataset
mynoiseq - Example of objects used and created by the NOISeq package

On BioConductor:NOISeq-2.57.0(bioc 3.24)NOISeq-2.56.0(bioc 3.23)

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

immunooncology rnaseq differentialexpression visualization sequencing

6.98 score 5 packages 320 scripts 321 mentions 17 exports 5 dependencies

Last updated from:b6c243c063. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	137
linux-devel-x86_64	NOTE	185
source / vignettes	OK	176
linux-release-x86_64	NOTE	164
macos-release-arm64	NOTE	116
macos-oldrel-arm64	NOTE	98
windows-devel	NOTE	117
windows-release	NOTE	121
windows-oldrel	NOTE	125
wasm-release	OK	97

Exports:addData ARSyNseq dat dat2save DE.plot degenes explo.plot filtered.data noiseq noiseqbio PCA.GENES QCreport readData rpkm show tmm uqua

Dependencies:Biobase BiocGenerics generics lattice Matrix

NOISeq User's Guide

Rendered fromNOISeq.Rnwusingutils::Sweave

Last update: 2018-10-15
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ASCA Removal of Systematic Noise on Seq data	ARSyNseq arsynseq
Biodetection class	Biodetection Biodetection-class dat2save,Biodetection-method explo.plot,Biodetection-method show,Biodetection-method
CD class	CD CD-class dat2save,CD-method explo.plot,CD-method show,CD-method
CountsBio class	CountsBio CountsBio-class dat2save,CountsBio-method explo.plot,CountsBio-method show,CountsBio-method
Exploration of expression data.	dat
Saving data generated for exploratory plots.	dat2save
Recovering differencially expressed features.	degenes
Plotting differential expression results	DE.plot
Example of objects used and created by the NOISeq package	mydata mynoiseq
Exploratory plots for expression data.	explo.plot
Methods to filter out low count features	filtered.data
GCbias class	dat2save,GCbias-method explo.plot,GCbias-method GCbias GCbias-class show,GCbias-method
lengthbias class	dat2save,lengthbias-method explo.plot,lengthbias-method lengthbias lengthbias-class show,lengthbias-method
Marioni's dataset	mybiotypes mychroms mycounts myfactors mygc mylength
Class myCounts	myCounts myCounts-class
Differential expression method for technical replicates or no replicates at all	noiseq
Differential expression method for biological replicates	noiseqbio
Normalization methods	rpkm tmm uqua
Output class of NOISeq	Output Output-class show,Output-method
PCA class	dat2save,PCA-method explo.plot,PCA-method PCA PCA-class show,PCA-method
Principal Component Analysis	PCA.GENES
Quality Control report for expression data	QCreport
Creating an object of eSet class	addData readData
Saturation class	dat2save,Saturation-method explo.plot,Saturation-method Saturation saturation Saturation-class show,Saturation-method