Package: consensusSeekeR
Version: 1.0.2
Date: 2015-05-01
Title: Detection of consensus regions inside a group of experiences
using genomic positions and genomic ranges
Description: This package compares genomic positions and genomic ranges from
multiple experiments to extract common regions. The size of the analyzed region
is adjustable as well as the number of experiences in which a feature must be
present in a potential region to tag this region as a consensus region.
Author: Astrid Deschenes [cre, aut], Fabien Claude Lamaze [ctb], Pascal Belleau
[aut], Arnaud Droit [aut]
Author@R: c(person("Astrid", "Deschenes", email="Astrid-
Louise.Deschenes@crchudequebec.ulaval.ca",
role=c("cre","aut")), person("Fabien Claude", "Lamaze",
email="fabien.lamaze.1@ulaval.ca", role=c("ctb")),
person("Pascal", "Belleau",
email="pascal.belleau@crchuq.ulaval.ca", role=c("aut")),
person("Arnaud", "Droit",
email="arnaud.droit@crchuq.ulaval.ca", role=c("aut")))
Depends: R (>= 2.10), BiocGenerics, IRanges, GenomicRanges, BiocParallel
Imports: GenomeInfoDb, rtracklayer, stringr, S4Vectors
Suggests: BiocStyle, ggplot2, knitr, RUnit
License: Artistic-2.0
URL: https://github.com/ArnaudDroitLab/consensusSeekeR
BugReports: https://github.com/ArnaudDroitLab/consensusSeekeR/issues
VignetteBuilder: knitr
NeedsCompilation: no
biocViews: BiologicalQuestion, ChIPSeq, Genetics, MultipleComparison,
Transcription, PeakDetection, Sequencing, Coverage
Maintainer: Astrid Louise Deschenes <Astrid-Louise.Deschenes@crchudequebec.ulaval.ca>
RoxygenNote: 5.0.1
Packaged: 2016-05-16 05:51:37 UTC; biocbuild
Package: doppelgangR
Maintainer: Levi Waldron <lwaldron.research@gmail.com>
Depends: R (>= 3.3), Biobase, BiocParallel
Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, ROCR, pROC, RUnit, simulatorZ, proxy
Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, utils
Author: Levi Waldron, Markus Riester, Marcel Ramos
Version: 1.0.2
Date: 2016-03-14
License: GPL (>=2.0)
Title: Identify likely duplicate samples from genomic or meta-data
Description: The main function is doppelgangR(), which takes as minimal
input a list of ExpressionSet object, and searches all list
pairs for duplicated samples. The search is based on the
genomic data (exprs(eset)), phenotype/clinical data
(pData(eset)), and "smoking guns" - supposedly unique
identifiers found in pData(eset).
URL: https://github.com/lwaldron/doppelgangR
BugReports: https://github.com/lwaldron/doppelgangR/issues
VignetteBuilder: knitr
biocViews: RNASeq, Microarray, GeneExpression, QualityControl
NeedsCompilation: no
Packaged: 2016-05-16 06:02:03 UTC; biocbuild
Package: ClassifyR
Type: Package
Title: A framework for two-class classification problems, with
applications to differential variability and differential
distribution testing
Version: 1.6.2
Date: 2016-03-08
Author: Dario Strbenac, John Ormerod, Graham Mann, Jean Yang
Maintainer: Dario Strbenac <dario.strbenac@sydney.edu.au>
VignetteBuilder: knitr
biocViews: Classification, Survival
Depends: R (>= 3.0.3), methods, Biobase, BiocParallel
Imports: locfit, ROCR, grid
Suggests: limma, edgeR, car, Rmixmod, ggplot2 (>= 2.0.0), gridExtra (>=
2.0.0), BiocStyle, pamr, sparsediscrim, PoiClaClu, curatedOvarianData, parathyroidSE, knitr, klaR, gtable, scales, e1071, rmarkdown, IRanges
Description: The software formalises a framework for classification in R.
There are four stages; Data transformation, feature selection, classifier training,
and prediction. The requirements of variable types and names are
fixed, but specialised variables for functions can also be provided.
The classification framework is wrapped in a driver loop, that
reproducibly carries out a number of cross-validation schemes.
Functions for differential expression, differential variability,
and differential distribution are included. Additional functions
may be developed by the user, by creating an interface to the framework.
Collate: bartlettSelection.R classes.R utilities.R calcPerformance.R
classifyInterface.R DMDselection.R edgeRselection.R errorMap.R
fisherDiscriminant.R distribution.R getLocationsAndScales.R
KolmogorovSmirnovSelection.R KullbackLeiblerSelection.R
leveneSelection.R likelihoodRatioSelection.R limmaSelection.R
mixmodels.R naiveBayesKernel.R
nearestShrunkenCentroidSelectionInterface.R
nearestShrunkenCentroidTrainInterface.R
nearestShrunkenCentroidPredictInterface.R performancePlot.R
plotFeatureClasses.R previousSelection.R rankingPlot.R
ROCplot.R runTest.R runTests.R selectionPlot.R
subtractFromLocation.R
License: GPL-3
Packaged: 2016-05-16 04:45:32 UTC; biocbuild
NeedsCompilation: no
Package: CopywriteR
Type: Package
Title: Copy number information from targeted sequencing using
off-target reads
Version: 2.4.0
Date: 2016-02-23
Author: Thomas Kuilman
Maintainer: Thomas Kuilman <t.kuilman@nki.nl>
Imports: matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges, Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges, CopyhelpeR, GenomeInfoDb, futile.logger
Depends: R (>= 3.2), BiocParallel
Suggests: BiocStyle, SCLCBam, snow
URL: https://github.com/PeeperLab/CopywriteR
Description: CopywriteR extracts DNA copy number information from targeted sequencing by utiizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.
License: GPL-2
biocViews: TargetedResequencing, ExomeSeq, CopyNumberVariation,
Preprocessing, Visualization, Coverage
NeedsCompilation: no
Packaged: 2016-05-04 06:16:03 UTC; biocbuild
Package: DEXSeq
Version: 1.18.4
Title: Inference of differential exon usage in RNA-Seq
Author: Simon Anders <sanders@fs.tum.de> and Alejandro Reyes
<alejandro.reyes@embl.de>
Maintainer: Alejandro Reyes <alejandro.reyes@embl.de>
Imports: BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter
Depends: BiocParallel, Biobase, SummarizedExperiment, IRanges (>=
2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.9.11), AnnotationDbi, RColorBrewer, S4Vectors
Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr
Enhances:
Description: The package is focused on finding differential exon usage
using RNA-seq exon counts between samples with different
experimental designs. It provides functions that allows the
user to make the necessary statistical tests based on a model
that uses the negative binomial distribution to estimate the
variance between biological replicates and generalized linear
models for testing. The package also provides functions for the
visualization and exploration of the results.
License: GPL (>= 3)
URL:
biocViews: Sequencing, RNASeq, DifferentialExpression
Packaged: 2016-05-19 02:54:44 UTC; biocbuild
VignetteBuilder: knitr
NeedsCompilation: no
Package: Oscope
Type: Package
Title: Oscope - A statistical pipeline for identifying oscillatory
genes in unsynchronized single cell RNA-seq
Version: 1.2.0
Date: 2015-7-28
Author: Ning Leng
Maintainer: Ning Leng <lengning1@gmail.com>
Depends: EBSeq, cluster, testthat, BiocParallel
Suggests: BiocStyle
Description: Oscope is a statistical pipeline developed to identifying
and recovering the base cycle profiles of oscillating genes in
an unsynchronized single cell RNA-seq experiment. The Oscope
pipeline includes three modules: a sine model module to search
for candidate oscillator pairs; a K-medoids clustering module
to cluster candidate oscillators into groups; and an extended
nearest insertion module to recover the base cycle order for
each oscillator group.
License: Artistic-2.0
Collate: 'AbsCor.R' 'NormForSine.R' 'SineFun.R' 'FormatSineOut.R'
'Opt2Shift.R' 'SineOptim.R' 'PipeR.R' 'ImpShift.R'
'PipeShiftCDF.R' 'scanK.R' 'NISFun.R' 'CalcMV.R' 'OscopeKM.R'
'OscopeENI.R' 'OscopeSine.R' 'FlagCluster.R' 'PermuCut.R'
BuildVignettes: yes
biocViews: StatisticalMethod,RNASeq, Sequencing, GeneExpression
NeedsCompilation: no
Packaged: 2016-05-04 06:27:29 UTC; biocbuild