Package: doseR 1.21.0

ake.vastermark

doseR: doseR

doseR package is a next generation sequencing package for sex chromosome dosage compensation which can be applied broadly to detect shifts in gene expression among an arbitrary number of pre-defined groups of loci. doseR is a differential gene expression package for count data, that detects directional shifts in expression for multiple, specific subsets of genes, broad utility in systems biology research. doseR has been prepared to manage the nature of the data and the desired set of inferences. doseR uses S4 classes to store count data from sequencing experiment. It contains functions to normalize and filter count data, as well as to plot and calculate statistics of count data. It contains a framework for linear modeling of count data. The package has been tested using real and simulated data.

Authors:AJ Vaestermark, JR Walters.

doseR_1.21.0.tar.gz
doseR_1.21.0.zip(r-4.5)doseR_1.21.0.zip(r-4.4)doseR_1.21.0.zip(r-4.3)
doseR_1.21.0.tgz(r-4.4-any)doseR_1.21.0.tgz(r-4.3-any)
doseR_1.21.0.tar.gz(r-4.5-noble)doseR_1.21.0.tar.gz(r-4.4-noble)
doseR_1.21.0.tgz(r-4.4-emscripten)doseR_1.21.0.tgz(r-4.3-emscripten)
doseR.pdf |doseR.html✨
doseR/json (API)
NEWS

# Install 'doseR' in R:

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

Datasets:

hmel.dat - Hmel data set
se - Hmel data set

On BioConductor:doseR-1.21.0(bioc 3.20)doseR-1.20.0(bioc 3.19)

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

bioconductor-package

14 exports 0.71 score 43 dependencies

Last updated 2 months agofrom:3341ce2043

Exports:dafsFilter generateStats getLibsizes3 glSeq iqrxFilter make_RPKM plotExpr plotMA.se plotRatioBoxes plotRatioDensity quantFilter se.DM simpleFilter test_diffs

Dependencies:abind askpass Biobase BiocGenerics boot crayon curl DelayedArray digest edgeR GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite lattice limma lme4 locfit MASS Matrix MatrixGenerics matrixStats mclust mime minqa nlme nloptr openssl R6 Rcpp RcppEigen RUnit S4Arrays S4Vectors SparseArray statmod SummarizedExperiment sys UCSC.utils XVector zlibbioc

doseR

AJ Vaestermark, JR Walters.

Rendered fromdoseR.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2019-03-05
Started: 2019-01-24

Help page	Topics
dafs	dafs
dafsFilter Function to filter expression data within an object.	dafsFilter
generateStats Statistics function to summarize expression data of an s.e. object.	generateStats
getLibsizes3 Get Lib Sizes.	getLibsizes3
glSeq LME4 wrapper.	glSeq
Hmel data set	hmel.dat
iqrxFilter Function to filter expression data within an s.e. object.	iqrxFilter
make_RPKM Make RPKM.	make_RPKM
plotExpr Function to generate a boxplot (expression) for a SummarizedExperiment object based on the replicate data.	plotExpr
plotMA.se Function to make MA plot.	plotMA.se
plotRatioBoxes Function to boxplot density of ratios between two treatments (using groupings from an annotation column) within a SummarizedExperiment object.	plotRatioBoxes
plotRatioDensity Function to plot density of ratios between two treatments (using groupings from an annotation column) within an object.	plotRatioDensity
quantFilter Function to filter expression data of a SummarizedExperiment object.	quantFilter
Hmel data set	se
se.DM Function to convert SummarizedExperiment object to LME4 input.	se.DM
simpleFilter Function to filter expression data of an object.	simpleFilter
test_diffs Statistics function to summarize expression data of an object, using ratios between selected treatments.	test_diffs

Package: doseR 1.21.0

doseR: doseR

doseR

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Help Manual

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