API for LTLA/csaw
ChIP-Seq Analysis with Windows
| Global functions | |
|---|---|
| $,readParam-method | Man page |
| .activeChrs | Source code |
| .checkLibSizes | Source code |
| .checkNestedRanges | Source code |
| .check_bimodality | Source code |
| .coerceFragments | Source code |
| .collateExt | Source code |
| .correlate_reads | Source code |
| .decideStrand | Source code |
| .extendSE | Source code |
| .extendSEdir | Source code |
| .extractPE | Source code |
| .extractSE | Source code |
| .fetch_norm_details | Source code |
| .formatColData | Source code |
| .general_test_combiner | Source code |
| .getDiscard | Source code |
| .getGlobalBg | Source code |
| .getPValCol | Source code |
| .getWindowNum | Source code |
| .get_total_pts | Source code |
| .get_two_one_sided_results | Source code |
| .is_pt_at_start | Source code |
| .make_BamFile | Source code |
| .make_BamFiles | Source code |
| .make_one_sided | Source code |
| .overlapStats | Source code |
| .parseFCcol | Source code |
| .profile_sites | Source code |
| .region_counts | Source code |
| .setupDiscard | Source code |
| .toGRanges | Source code |
| .verify_ranges_tabs | Source code |
| .weightedFDR | Source code |
| .window_counts | Source code |
| asDGEList | Man page |
| asDGEList,SummarizedExperiment-method | Man page |
| calculateCPM | Man page Source code |
| checkBimodality | Man page Source code |
| cluster-direction | Man page |
| clusterFDR | Man page Source code |
| clusterWindows | Man page Source code |
| clusterWindowsList | Man page Source code |
| combineOverlaps | Man page Source code |
| combineTests | Man page Source code |
| consolidateOverlaps | Man page Source code |
| consolidateTests | Man page Source code |
| consolidateWindows | Man page Source code |
| controlClusterFDR | Man page Source code |
| correlateReads | Man page Source code |
| csaw | Man page |
| csawUsersGuide | Man page Source code |
| defunct | Man page |
| detailRanges | Man page Source code |
| empiricalFDR | Man page Source code |
| empiricalOverlaps | Man page Source code |
| extractReads | Man page Source code |
| filterWindows | Man page Source code |
| filterWindowsControl | Man page Source code |
| filterWindowsGlobal | Man page Source code |
| filterWindowsLocal | Man page Source code |
| filterWindowsProportion | Man page Source code |
| findMaxima | Man page Source code |
| findOverlapsList | Man page Source code |
| getBestOverlaps | Man page Source code |
| getBestTest | Man page Source code |
| getPESizes | Man page Source code |
| getWidths | Man page Source code |
| maximizeCcf | Man page Source code |
| mergeResults | Man page Source code |
| mergeResultsList | Man page Source code |
| mergeWindows | Man page Source code |
| mergeWindowsList | Man page Source code |
| minimalTests | Man page Source code |
| mixedClusters | Man page Source code |
| mixedOverlaps | Man page Source code |
| mixedTests | Man page Source code |
| normFactors | Man page Source code |
| normOffsets | Man page Source code |
| overlapResults | Man page Source code |
| overlapResultsList | Man page Source code |
| overlapStats | Man page |
| profileSites | Man page Source code |
| readParam | Man page Source code |
| readParam-class | Man page |
| reform | Man page |
| reform,readParam-method | Man page |
| regionCounts | Man page Source code |
| scaleControlFilter | Man page Source code |
| scaledAverage | Man page Source code |
| show,readParam-method | Man page |
| strandedCounts | Man page Source code |
| summitOverlaps | Man page Source code |
| upweightSummit | Man page Source code |
| windowCounts | Man page Source code |
| wwhm | Man page Source code |
