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.

Author
Sonia Tarazona, Pedro Furio-Tari, Maria Jose Nueda, Alberto Ferrer and Ana Conesa
Date of publication
None
Maintainer
Sonia Tarazona <starazona@cipf.es>
License
Artistic-2.0
Version
2.18.0

View on Bioconductor

Man pages

ARSyNSeq
ASCA Removal of Systematic Noise on Seq data
Biodetection
Biodetection class
CD
CD class
CountsBio
CountsBio class
dat
Exploration of expression data.
dat2save
Saving data generated for exploratory plots.
degenes
Recovering differencially expressed features.
DE.plot
Plotting differential expression results
example
Example of objects used and created by the NOISeq package
explo.plot
Exploratory plots for expression data.
filter.low.counts
Methods to filter out low count features
GCcontentBias
GCbias class
LengthBias
lengthbias class
Marioni
Marioni's dataset
myCounts
Class myCounts
noiseq
Differential expression method for technical replicates or no...
noiseqbio
Differential expression method for biological replicates
normalization
Normalization methods
Output
Output class of NOISeq
PCA
PCA class
PCA.GENES
Principal Component Analysis
QCreport
Quality Control report for expression data
readData
Creating an object of eSet class
Saturation
Saturation class

Files in this package

NOISeq/.Rinstignore
NOISeq/DESCRIPTION
NOISeq/NAMESPACE
NOISeq/NEWS
NOISeq/R
NOISeq/R/ARSyNcomponents.R
NOISeq/R/ARSyNmodel.R
NOISeq/R/ARSyNseq.R
NOISeq/R/ASCA1f.R
NOISeq/R/ASCA2f.R
NOISeq/R/ASCA3f.R
NOISeq/R/ASCAfun-triple.R
NOISeq/R/ASCAfun1.R
NOISeq/R/ASCAfun12.R
NOISeq/R/ASCAfun2.R
NOISeq/R/ASCAfunres.R
NOISeq/R/DE.plot.R
NOISeq/R/GC.bias.plot.R
NOISeq/R/MD.R
NOISeq/R/MD.plot.R
NOISeq/R/PCA.GENES.R
NOISeq/R/PCA.plot.R
NOISeq/R/QCreport.R
NOISeq/R/allMD.R
NOISeq/R/auxiliar.R
NOISeq/R/biodetection.plot.R
NOISeq/R/cd.plot.R
NOISeq/R/classes.R
NOISeq/R/countsbio.plot.R
NOISeq/R/dat.R
NOISeq/R/degenes.R
NOISeq/R/fewreplicates.R
NOISeq/R/filter.low.counts.R
NOISeq/R/length.bias.plot.R
NOISeq/R/makeASCAdesign.R
NOISeq/R/noiseq.R
NOISeq/R/noiseqbio.R
NOISeq/R/normalization.R
NOISeq/R/probdeg.R
NOISeq/R/readData.R
NOISeq/R/saturation.plot.R
NOISeq/build
NOISeq/build/vignette.rds
NOISeq/data
NOISeq/data/Marioni.RData
NOISeq/data/myCounts.RData
NOISeq/data/noiseq.RData
NOISeq/inst
NOISeq/inst/CITATION
NOISeq/inst/doc
NOISeq/inst/doc/NOISeq.R
NOISeq/inst/doc/NOISeq.Rnw
NOISeq/inst/doc/NOISeq.pdf
NOISeq/inst/doc/QCreport.pdf
NOISeq/man
NOISeq/man/ARSyNSeq.Rd
NOISeq/man/Biodetection.Rd
NOISeq/man/CD.Rd
NOISeq/man/CountsBio.Rd
NOISeq/man/DE.plot.Rd
NOISeq/man/GCcontentBias.Rd
NOISeq/man/LengthBias.Rd
NOISeq/man/Marioni.Rd
NOISeq/man/Output.Rd
NOISeq/man/PCA.GENES.Rd
NOISeq/man/PCA.Rd
NOISeq/man/QCreport.Rd
NOISeq/man/Saturation.Rd
NOISeq/man/dat.Rd
NOISeq/man/dat2save.Rd
NOISeq/man/degenes.Rd
NOISeq/man/example.Rd
NOISeq/man/explo.plot.Rd
NOISeq/man/filter.low.counts.Rd
NOISeq/man/myCounts.Rd
NOISeq/man/noiseq.Rd
NOISeq/man/noiseqbio.Rd
NOISeq/man/normalization.Rd
NOISeq/man/readData.Rd
NOISeq/vignettes
NOISeq/vignettes/NOISeq.Rnw