API for mzytnicki/msscaf
Multiple-source scaffolder
| Global functions | |
|---|---|
| ..addJoinPlots | Source code |
| ..checkCorners | Source code |
| ..compareBreaks | Source code |
| .addJoinPlots | Source code |
| .addScaffold | Source code |
| .checkBreaks | Source code |
| .checkCorners | Source code |
| .checkJoins | Source code |
| .compareBreaks | Source code |
| .computeBreakPvalue | Source code |
| .computeNCells | Source code |
| .estimateBackgroundCounts | Source code |
| .estimateMetaBinsMoleculeSize | Source code |
| .estimateMetaSizes | Source code |
| .estimateMoleculeSize | Source code |
| .estimateRowCount | Source code |
| .filterBreaks | Source code |
| .keepScaffolds | Source code |
| .mergeBreaks | Source code |
| .normalizeHighCountRows | Source code |
| .notSquareICE | Source code |
| .removeAmbiguousJoins | Source code |
| .removeLowCount | Source code |
| .removeLowCountRows | Source code |
| .removeSmallScaffoldsOutlierBins | Source code |
| .scaffold | Source code |
| .stitchChromosomePair | Source code |
| ICE | Source code |
| KR | Source code |
| addExp | Source code |
| addJoin | Source code |
| addJoinPlots | Source code |
| addJoins | Source code |
| addNoise | Source code |
| addSplit | Source code |
| addSplits | Source code |
| checkAllBinDifference | Source code |
| checkAllOutlierBins | Source code |
| checkBinDifference | Source code |
| checkBreaks | Source code |
| checkCorners | Source code |
| checkInsertions | Source code |
| checkJoins | Source code |
| checkMatrices | Source code |
| checkMatrix | Source code |
| checkOutlierBins | Source code |
| checkSizeDifference | Source code |
| classifyCornerPointsCpp | Source code |
| cleanData | Source code |
| cleanMatrices | Source code |
| compareBreaks | Source code |
| computeBreakPvalue | Source code |
| computeCornerDifferenceBothOffsetCpp | Source code |
| computeCornerDifferenceOffsetCpp | Source code |
| computeCornerSize | Source code |
| computeInsertion | Source code |
| computeInsertionBinDepth | Source code |
| computeInsertionDepth | Source code |
| computeMeanTrianglesCpp | Source code |
| computeNCells | Source code |
| computeNRrows | Source code |
| computeOtherSize | Source code |
| computePValue | Source code |
| computeRefSizes | Source code |
| computeRefSizesCpp | Source code |
| computeSample | Source code |
| computeScaleFactor | Source code |
| computeSymmetricColSum | Source code |
| computeSymmetricColSumMeta | Source code |
| computeTest | Source code |
| create2Ref | Source code |
| createScaffoldPlaces | Source code |
| discardJoinsFromRefRef | Source code |
| estimateBackgroundCounts | Source code |
| estimateDistanceCountCpp | Source code |
| estimateMaxMoleculeSizeCpp | Source code |
| estimateMetaBinsMoleculeSize | Source code |
| estimateMetaBinsMoleculeSizeCpp | Source code |
| estimateMetaSizeCpp | Source code |
| estimateMetaSizes | Source code |
| estimateMoleculeSize | Source code |
| estimateMoleculeSizeCpp | Source code |
| estimateRowCount | Source code |
| extract2Ref | Source code |
| extractCorner | Source code |
| extractCornersCpp | Source code |
| extractCornersFullCpp | Source code |
| extractLines | Source code |
| extractRef | Source code |
| fillCorner | Source code |
| filterBreak | Source code |
| filterBreaks | Source code |
| filterCornersCpp | Source code |
| findJoins | Source code |
| generateCorner | Source code |
| generateJoin | Source code |
| generateSplit | Source code |
| getDataset | Source code |
| getDatasetRef | Source code |
| getJoinInfo | Source code |
| getNInteractionsPerRef | Source code |
| getRefOrders | Source code |
| isMatrixEmpty | Source code |
| keepScaffolds | Source code |
| keepScaffoldsCpp | Source code |
| keepScaffoldsPairsCpp | Source code |
| makeFullMatrix | Source code |
| makeFullMatrixGenome | Source code |
| makeFullTibble | Source code |
| makeFullTibbleNotSquare | Source code |
| makeSparseMatrix | Source code |
| makeSparseMatrixGenome | Source code |
| makeSymmetric | Source code |
| makeSymmetricRefCpp | Source code |
| makeTibbleFromList | Source code |
| mergeBreaks | Source code |
| mergeJoins | Source code |
| mergeRefs | Source code |
| mergeSizes | Source code |
| msscaf | Source code |
| msscaf2RefExp | Source code |
| msscafData | Source code |
| msscafRefExp | Source code |
| normalize | Source code |
| normalizeAndInsertion | Source code |
| normalizeHighCountRows | Source code |
| normalizeHighCountRowsCpp | Source code |
| normalizeKR | Source code |
| normalizeMD | Source code |
| normalizeNotSquareICE | Source code |
| normalizeRefs | Source code |
| notSquareICE | Source code |
| orderJoins | Source code |
| parseBamFile | Source code |
| parseBamFileCpp | Source code |
| parseCoolFile | Source code |
| parseHicCpp | Source code |
| parseHicFile | Source code |
| parsePafCpp | Source code |
| parsePafFile | Source code |
| plotMoleculeSizeDistribution | Source code |
| removeAmbiguousJoins | Source code |
| removeFarFromDiagonal | Source code |
| removeLowCount | Source code |
| removeLowCountRows | Source code |
| removeLowCountRowsCpp | Source code |
| removeNearEqualBreaks | Source code |
| removeNearEqualBreaksCpp | Source code |
| removeOutliersCpp | Source code |
| removeOutliersRef | Source code |
| removeOutliersRefCpp | Source code |
| removeSmallScaffolds | Source code |
| removeSuboptimalJoins | Source code |
| repairJoins | Source code |
| rescale | Source code |
| rescaleValue | Source code |
| sampleTriangles | Source code |
| scaffold | Source code |
| scaffoldContigs | Source code |
| scaffoldCounts | Source code |
| scaffoldSizes | Source code |
| selectJoins | Source code |
| smoothenDistribution | Source code |
| splitBy2Ref | Source code |
| splitBy2RefFromMatrix | Source code |
| splitByRef | Source code |
| splitChromosomeCpp | Source code |
| splitChromosomes | Source code |
| splitCpp | Source code |
| stitchChromosomePair | Source code |
| sumCornerCpp | Source code |
| testJoin | Source code |
| transformRefAfterToRefRef | Source code |
| updateRefs | Source code |
