Man pages for alexjgriffith/CCCA
Cross Condition ChIP Analyisis
| addColnames | Add Column Names |
| addFasta | Add Fasta |
| addNames | Add Names |
| addRownames | Add Row Names |
| andM | and for Matrix |
| applyPeakPartitions | apply peak partitions |
| CCCA | Compare multiple ChIP data sets across experimental... |
| chromGenomeSort | Chrom Genome Sort |
| compliment | reverse compliment |
| consenusIUPAC | Consensus IUPAC |
| convertChroms | convertChroms |
| createZip | Create Zip |
| distanceBetweenMotifs | distanceBetweenMoitfs |
| findMotifDist | find motif distance |
| findSharedRegions | Find Shared Regions |
| genEboxCombs | Generate Ebox Combinations |
| geneRanges | Gene Ranges |
| geneRangeToRegion | Gene Range to Region |
| generate | Generate |
| genomicRegions | Genomic Regions |
| genSwapFun | genSwapFun |
| getData | getData |
| getDistance | getDistance |
| getHeights | Get Heights |
| getMotifInfo | Get Motif Info |
| getPileUp | getPileUp |
| greatGeneAssoc | Great Gene Assoc |
| grepMotifs | Grep Motifs |
| heightHist | Height Histrogram A plotting tool for histograms, Requires... |
| hg19Sort | hg19Sort |
| histVisualize | Visualize batches of height data |
| homerWrapper | Homer Wrapper |
| intersectN | instersect N |
| ispalandrome | Is Palandrome |
| IUPACtoBase | Turn IUPAC lables into basic neucleotides |
| loadBedFile | loadBedFile |
| loadPWM | Load PWM |
| locHist | Location Histogram A plotting tool for histograms, Requires... |
| locHist2 | locHist |
| lzip | List Zip |
| makeAFS | Make AFS |
| makeLogic | Make Logical |
| makeTable | make table |
| mapziplist | map zip list |
| mLength | m Length |
| modulous | modulous |
| mor | method or |
| motifDistances | motif distances |
| motifHist | Motif histogram |
| motifs2View | Motifs Two View |
| motifString | Motif String |
| multiPlot | Multi Plot |
| mWidth | m Width |
| nearSummit | nearSummit |
| normalize | Normalize |
| numberIntersect | Intersect Count |
| orderBed | Order Bed |
| orM | orM |
| ors | ors |
| overlap | Overlap |
| pairwiseCombs | pariwise Combinations |
| pass | Pass |
| pca | PCA |
| peakPartitions | peak partitions |
| peakRegions | peak Regions #experimental |
| pileUp | PileUp |
| plotPCs | plot PCs |
| PWMtoCons | PWM to Consensus Motif |
| qn | Quantile Normalization |
| qstem | Quick Stem Plot |
| rankChroms | rankChroms |
| readCategories | Read Categories |
| regionWrapper | region wrapper #experimental |
| reverseIUPAC | reverse IUPAC |
| sel2 | Select Second |
| sepAxis | seperate axis |
| shiftFromZero | Shift from zero |
| simpleSwapFun | simple swap fun |
| sortDataFrame | sort data frame |
| splitBlist | Split by List |
| splitZip | Split Zip |
| stem | stem |
| stringToSwap | string to swap fun |
| unifyBedFile | unify bed file |
| unionN | union N |
| unityOutput | unity output |
