as.class.vector         Create a class vector
build.export            Results export builder
calc.f1score            Calculate the F1-score
calc.otr                Calculate the ratio TP/(FP+FN)
cddat                   Old functions from NOISeq
cdplot                  Old functions from NOISeq
check.contrast.format   Contrast validator
check.file.args         File argument validator
check.graphics.file     Check graphics file
check.graphics.type     Check plotting device
check.libsize           Library size validator
check.main.args         Main argument validator
check.num.args          Numeric argument validator
check.packages          Required packages validator
check.parallel          Parallel run validator
check.text.args         Text argument validator
combine.bonferroni      Combine p-values with Bonferroni's method
combine.maxp            Combine p-values using the maximum p-value
combine.minp            Combine p-values using the minimum p-value
combine.simes           Combine p-values with Simes' method
combine.weight          Combine p-values using weights
construct.gene.model    Assemble a gene model based on exon counts
diagplot.avg.ftd        Create average False (or True) Discovery curves
diagplot.boxplot        Boxplots wrapper for the metaseqR package
diagplot.cor            Summarized correlation plots
diagplot.de.heatmap     Diagnostic heatmap of differentially expressed
                        genes
diagplot.edaseq         Diagnostic plots based on the EDASeq package
diagplot.filtered       Diagnostic plot for filtered genes
diagplot.ftd            Create False (or True) Positive (or Negative)
                        curves
diagplot.mds            Multi-Dimensinal Scale plots or RNA-Seq samples
diagplot.metaseqr       Diagnostic plots for the metaseqR package
diagplot.noiseq         Diagnostic plots based on the NOISeq package
diagplot.noiseq.saturation
                        Simpler implementation of saturation plots
                        inspired from NOISeq package
diagplot.pairs          Massive X-Y, M-D correlation plots
diagplot.roc            Create basic ROC curves
diagplot.venn           Venn diagrams when performing meta-analysis
diagplot.volcano        (Interactive) volcano plots of differentially
                        expressed genes
disp                    Message displayer
downsample.counts       Downsample read counts
estimate.aufc.weights   Estimate AUFC weights
estimate.sim.params     Estimate negative binomial parameters from real
                        data
filter.exons            Filter gene expression based on exon counts
filter.genes            Filter gene expression based on gene counts
filter.high             Filtering helper
filter.low              Filtering helper
fisher.method           Perform Fisher's Method for combining p-values
fisher.method.perm      Derive a p-value for a summary statistic of
                        p-values by permutation
fisher.sum              A function to calculate Fisher's sum for a set
                        of p-values
get.annotation          Annotation downloader
get.arg                 Argument getter
get.biotypes            Biotype converter
get.bs.organism         Return a proper formatted BSgenome organism
                        name
get.dataset             Annotation downloader helper
get.defaults            Default parameters for several metaseqr
                        functions
get.ensembl.annotation
                        Ensembl annotation downloader
get.exon.attributes     Annotation downloader helper
get.gc.content          Return a named vector of GC-content for each
                        genomic region
get.gene.attributes     Annotation downloader helper
get.host                Annotation downloader helper
get.preset.opts         Return several analysis options given an
                        analysis preset
get.strict.biofilter    Group together a more strict biotype filter
get.ucsc.annotation     UCSC/RefSeq annotation downloader
get.ucsc.credentials    Return host, username and password for UCSC
                        Genome Browser database
get.ucsc.dbl            Download annotation from UCSC servers,
                        according to organism and source
get.ucsc.organism       Return a proper formatted organism alias
get.ucsc.query          Return queries for the UCSC Genome Browser
                        database, according to organism and source
get.ucsc.tabledef       Get SQLite UCSC table defintions, according to
                        organism and source
get.ucsc.tbl.tpl        Create SQLite UCSC table template defintions
get.valid.chrs          Annotation downloader helper
get.weights             Get precalculated statistical test weights
graphics.close          Close plotting device
graphics.open           Open plotting device
hg19.exon.counts        Human RNA-Seq data with three conditions, three
                        samples
libsize.list.hg19       Human RNA-Seq data with three conditions, three
                        samples
libsize.list.mm9        Mouse RNA-Seq data with two conditions, four
                        samples
load.bs.genome          Loads (or downloads) the required BSGenome
                        package
log2disp                Display value transformation
make.avg.expression     Calculates fold changes
make.contrast.list      Create contrast lists from contrast vectors
make.export.list        Intitialize output list
make.fold.change        Calculates fold changes
make.grid               Optimize rectangular grid plots
make.highcharts.points
                        Interactive volcano plot helper
make.html.body          HTML report helper
make.html.cells         HTML report helper
make.html.header        HTML report helper
make.html.rows          HTML report helper
make.html.table         HTML report helper
make.matrix             Results output build helper
make.path.struct        Project path constructor helper
make.permutation        Create counts matrix permutations
make.project.path       Project path constructor
make.report.messages    Initializer of report messages
make.sample.list        Creates sample list from file
make.sim.data.sd        Create simulated counts using the
                        Soneson-Delorenzi method
make.sim.data.tcc       Create simulated counts using TCC package
make.stat               Calculates several statistices on read counts
make.transformation     Calculates several transformation of counts
make.venn.areas         Helper for Venn diagrams
make.venn.colorscheme   Helper for Venn diagrams
make.venn.counts        Helper for Venn diagrams
make.venn.pairs         Helper for Venn diagrams
meta.perm               Permutation tests for meta-analysis
meta.test               Meta-analysis using several RNA-Seq statistics
meta.worker             Permutation tests helper
metaseqR-package        The metaseqR Package
metaseqr                The main metaseqr pipeline
mlfo                    MLE dispersion estimate
mm9.gene.counts         mouse RNA-Seq data with two conditions, four
                        samples
nat2log                 General value transformation
normalize.deseq         Normalization based on the DESeq package
normalize.edaseq        Normalization based on the EDASeq package
normalize.edger         Normalization based on the edgeR package
normalize.nbpseq        Normalization based on the NBPSeq package
normalize.noiseq        Normalization based on the NOISeq package
read.targets            Creates sample list and BAM/BED file list from
                        file
read2count              SAM/BAM/BED file reader helper for the metaseqr
                        pipeline
reduce.exons            Merges exons to create a unique set of exons
                        for each gene
reduce.gene.data        Reduce the gene annotation in case of not all
                        chromosomes present in counts
sample.list.hg19        Human RNA-Seq data with three conditions, three
                        samples
sample.list.mm9         Mouse RNA-Seq data with two conditions, four
                        samples
set.arg                 Argument setter
stat.bayseq             Statistical testing with baySeq
stat.deseq              Statistical testing with DESeq
stat.edger              Statistical testing with edgeR
stat.limma              Statistical testing with limma
stat.nbpseq             Statistical testing with NBPSeq
stat.noiseq             Statistical testing with NOISeq
validate.alg.args       Validate normalization and statistical
                        algorithm arguments
validate.list.args      Validate list parameters for several metaseqR
                        functions
wapply                  List apply helper
wp.adjust               Multiple testing correction helper
