sort functions for BioC submission - Githubissues

fmicompbio / monaLisa

binned motif enrichment analysis and visualisation

https://fmicompbio.github.io/monaLisa/

GNU General Public License v3.0

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sort functions for BioC submission #46

Closed mbstadler closed 3 years ago

mbstadler commented 3 years ago

We'll not submit less mature/work-in-progress code.

[x] KEEP for submission

anno_seqlogo (make camel case?) bin calcBinnedMotifEnrHomer calcBinnedMotifEnrR findHomer findMotifHits getColsByBin homerToPFMatrixList parseHomerOutput plotBinDensity plotBinHist plotBinScatter plotMotifHeatmaps dumpJaspar seqLogoGrob getZeroBin setZeroBin sample_random_regions (make camel-case?) prepareHomer motifSimilarity plotSelectionProb plotStabilityPaths randLassoStabSel

calcBinnedKmerEnr getKmerFreq motifKmerSimilarity

[x] MOVE TO "Bart_with_kmers"

buildDirGraphFromKmers filterDirGraph getMotifsFromDirGraph clusterKmers (delete?) convertKmersToMotifs (delete?) extractOverlappingKmerFrequencies countKmerPairs countKmerPairsSelected
[x] DELETE

calcBinnedMotifEnr
[x] SPLIT vignette:
vignette 1: binned (motifs + kmers)
vignette 2: stability selection

mbstadler commented 3 years ago

This is all done now (v0.99.0)