Man pages for sebastian-gregoricchio/Rseb
An R-package for NGS data managing and visualization
| actualize | 'Rseb' updates verification |
| build.bed | Bed generator |
| calculate.mode | Mode calculation |
| closest.regions | Find closets regions to reference regions. |
| cmyk | CMYK color converter |
| CNV.data | CNV data results example |
| collapse.bed | Merger of overlapping peaks in a provided .bed file. |
| color.gradient | Gradient colors generation and assignment |
| combine.lists | List combiner |
| computeMatrix.deeptools | Score matrix NGS data builder at specific regions (by... |
| convert_sequence | Nucleic acid sequences converter. |
| data.frame.to.list | Data frame conversion to a list of columns. |
| data.summary | Statistical data summary generator |
| deeptools.matrix | deepTools matrix example |
| density.matrix | Density matrix builder |
| density_plot | Plot density signal of NGS data. |
| DE.status | Differential Expression status calculator for RNA-seq data |
| doughnut | Donut/Doughnut plot |
| evaluate.heterogeneity | Evaluate genomic heterogeneity among samples. |
| floating.ceiling | Ceiling to floating values |
| floating.floor | Flooring to floating values |
| genomic.tracks | Genomic tracks plotter |
| get.gene.name | Conversion of ENSEMBL gene IDs. |
| get.single.base.score.bw | Single base bigWig score selector |
| grepl.data.frame | Grep a pattern in a full data.frame. |
| GSEA.to.GOnumber | Conversion of GSEA terms into Gene Ontology numbers |
| IGVsnap | Script generator for Integrative Genomics Viewer (IGV) batch... |
| incucyte | Incucyte analysis tool |
| install.pkg.source | Package installer from source archive. |
| intersect.bedtools | Intersect two or more bed files (by 'bedtools intersect'... |
| intersect.regions | Genomic regions overlapper |
| is.color | is.color |
| is.nan_df | 'is.nan()' applied to a data.frame |
| mass.to.volume | Get solvent volume to make a solution with a given amount of... |
| molarity.to.mass | Get solvent volume to make a solution with a given amount of... |
| move.df.col | Function to change easily the order of specific columns in a... |
| multi.bigwig.mean | Multi-bigWig average tool |
| pkg.check | Check package installation. |
| pkg.version | Get session info and package versions. |
| plot.density.differences | Plot the distribution of overall NGS density at specific... |
| plot.density.profile | Plot of NGS density signal at specific regions from deepTools... |
| plot.density.profile.smooth | Plot of NGS density signal at specific regions from deepTools... |
| plot.density.summary | Plot the distribution of overall NGS density at specific... |
| plot.gsea | GSEA plotter |
| plot.multi.gsea | GSEA plotter |
| plot.NES | GSEA analyses NES plotter |
| pStars | P-value significance stars definer. |
| qPCR.results | qPCR RNA expression results example |
| qPCR.results.rep1 | qPCR RNA expression results example (rep1) |
| qPCR.results.rep2 | qPCR RNA expression results example (rep2) |
| qPCR.rna.exp | qPCR RNA expression analyses tool. |
| qPCR.rna.mean.reps | qPCR RNA expression experimental replicates mean calculator. |
| read.computeMatrix.file | 'computeMatrix' *.gz file reader |
| reorder.samples.computeMatrix | Sample reorderer computeMatrix file |
| restore_packages | Restores packages installed from a .rda file. |
| restriction.sites.to.bed | Generator of a bed file for enzymatic restriction sites. |
| RNAseq | RNA-seq example |
| sort.bed | Sorter function for .bed files. |
| store_packages | Stores the information of installed packages in a .rda file. |
| substract.bw | Combination of two or more list in a unique one. |
| uniform.x.axis | Plot X-axis uniforming |
| uniform.y.axis | Plot Y-axis uniforming |
| update_pkgs | function to automatically update the R packages. |
| venn.overlap | VennDiagram from region overlaps |
| volcano | Volcano plot generator for RNA-seq data. |
