| 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 |
| construct.utr.model | Assemble a gene model based on 3' UTR counts for quant-seq... |
| 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... |
| 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... |
| 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.transcript.utr.attributes | Annotation downloader helper |
| get.ucsc.annotation | UCSC/RefSeq annotation downloader |
| get.ucsc.credentials | Return host, username and password for UCSC Genome Browser... |
| get.ucsc.dbl | Download annotation from UCSC servers, according to organism... |
| get.ucsc.organism | Return a proper formatted organism alias |
| get.ucsc.query | Return queries for the UCSC Genome Browser database,... |
| get.ucsc.tabledef | Get SQLite UCSC table defintions, according to organism and... |
| 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 |
| metaseqr | The main metaseqr pipeline |
| metaseqR-package | The metaseqR Package |
| meta.test | Meta-analysis using several RNA-Seq statistics |
| meta.worker | Permutation tests helper |
| 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 |
| read2count | SAM/BAM/BED file reader helper for the metaseqr pipeline |
| read.targets | Creates sample list and BAM/BED file list from file |
| 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... |
| 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 |
