An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

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... |

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.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 |

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