Man pages for benja0x40/Tightrope
ChIP-seq normalization according to background reads density
| AddByRow | ** RESERVED FOR INTERNAL USE ** |
| BackgroundCandidates | Index of background candidates |
| bg_ranking | Average ranking for control measurements |
| BRD | Background Reads Density |
| BuildGeneFeatures | Build an R environment containing genomic features from... |
| BuildSeqInfo | Retrieve chromosome information from UCSC and build Seqinfo... |
| CDaDaDR.2D | Density estimation in reduced dimensions |
| CGI_hg38 | UCSC CGIs - Homo sapiens - GRCh38 / hg38 |
| CGI_mm10 | UCSC CGIs - Mus musculus - GRCm38 / mm10 |
| CleanupGRanges | Cleanup genomic ranges |
| ClonalArg | ** RESERVED FOR INTERNAL USE ** |
| ConsensusGRanges | Consensus genomic ranges |
| CoveredLength | Compute the genomic length covered by sequence reads |
| DefaultArgs | ** RESERVED FOR INTERNAL USE ** |
| DefaultOptions | ** RESERVED FOR INTERNAL USE ** |
| DefineSimulation | Define different populations for ChIP-seq simulations |
| DetectCounts | DetectCounts |
| df2grg | Convert 'data.frame' to GRanges |
| DitherCounts | Apply dithering to read counts |
| EGA91_human | Ensembl genes - Homo sapiens - GRCh38 / hg38 (rel. 91, Dec.... |
| EGA91_mouse | Ensembl genes - Mus musculus - GRCm38 / mm10 (rel. 91, Dec.... |
| FlatGRanges | Reduce genomic intervals |
| GenomicCoverage | Total coverage of genomic intervals |
| GenomicTiling | Whole genome tiling with regular bins (i.e. running windows) |
| hg38_blacklist | ENCODE blacklist - Homo sapiens - GRCh38 / hg38 |
| ImportCpGIslandExt | Import CpG-islands from UCSC genomes |
| ImportGenomicRanges | Import tab delimited text files representing genomic interval... |
| ImportLiftOverChain | Download and import UCSC's liftOver chain files |
| m2v | ** RESERVED FOR INTERNAL USE ** |
| MakeSimulation | Simulate ChIP-seq read count matrixes |
| mm10_blacklist | ENCODE blacklist - Mus musculus - GRCm38 / mm10 |
| MulByRow | ** RESERVED FOR INTERNAL USE ** |
| mv_emloop | Multivariate expectation-maximization |
| mv_expectation | Multivariate expectation |
| mv_gmm | Gaussian mixture model fitting |
| mv_init_param | Multivariate normal distribution: parameter initialization |
| mv_maximization | Multivariate maximization |
| mv_mle | Multivariate normal distribution: maximum likelihood... |
| mv_pdf | Multivariate normal distribution: probability density... |
| mv_rsg | Multivariate normal distribution: random sample generator |
| NonZeroCounts | Remove observations with missing values |
| NormalizeCountMatrix | Apply BRD scaling factors |
| NSC_K27M | H3K27me3 ChIP-seq in mouse Neuronal Stem Cell (NSCs) |
| PlotBRD | Control plots from BRD results |
| PlotCountDistributions | Plot empirical distributions of read counts |
| RandomCounts | Random counts |
| ReadCountMatrix | Compute read counts over genomic intervals for multiple bam... |
| RemoveOptions | ** RESERVED FOR INTERNAL USE ** |
| ResetOptions | ** RESERVED FOR INTERNAL USE ** |
| ScalingFactors | Get BRD scaling factors |
| Tightrope | Global options for Tightrope functions |
| v2m | ** RESERVED FOR INTERNAL USE ** |
| VectorArgs | ** RESERVED FOR INTERNAL USE ** |
| xy2md | Convert (x, y) to (a = mean, m = difference) coordinates |
