Man pages for ManchesterBioinference/Motif2Site
Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions
| Bed2Granges | Read a bed file as Genomic Ranges |
| combine2Table | Combine all IP and Input count table files |
| combineMotifFiles | Combine motif bed files into a combined ranges |
| combineTestResults | Combine count Table and statistics table |
| compareBedFiless2UserProvidedRegions | Compare a set of bed files to a user provided regions set |
| CompareBeds2GivenRegions | Compare a set of bed files to a provided regions set |
| CompareMotifs2GivenRegions | Comparison motifs locations to a given regions set |
| compareMotifs2UserProvidedRegions | Compare a set of motifs to a user provided regions set |
| computeFoldEnrichment | compute fold enrichment values for an experiment |
| data | Synthetic datasets used in the package |
| decomposeBindingSignal | Decompose binding signal among accepted motifs |
| DeleteMultipleFiles | Delete a vector of files |
| deriveHeuristicBindingDistribution | build heurisitc distribution around the binding sites |
| DetectBindingSites | Detect binding sites from motif |
| DetectBindingSitesBed | Detect binding sites from bed motif input |
| DetectBindingSitesMotif | Detect binding sites from sequence motif sequence and... |
| DetectFdrCutoffBH | FDR cut-off detection Benjamini Hochberg method |
| findMotifs | Find motif instances with a certain mismatch number |
| fitKernelDensity | Fit a kernel density distribution to the obersever heuristic... |
| generate1ntBedAlignment | Convert bam and bed files to 1 nucleotide bed |
| Motif2Site | Detect and Recenter binding sites from ChIP-seq experiments |
| motifBindingNegativeBinomialCount | Model IP and Input count values with negative Binomal |
| motifChipCount | count short reads related to each motif for a given ChIPseq... |
| motifCount | count short reads around motifs for all ChIP-seq experiments |
| motifTablePreProcess | Process count data and perform negative binomial test |
| NegativeBinomialTestWithReplicate | Negative binomial test of binding using all replicates |
| pairwisDifferential | Detect differential motifs |
| quiet | Suppress messages generated by in external package |
| recenterBindingSitesAcrossExperiments | Combine binding sites across experiments |
| removeNonBellShapedMotifs | Remove non-bell shpape motifs prior to binding signal... |
| strongestMotif | Returns the motif with the highest count |
