monaLisa package overview |
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monaLisa - MOtif aNAlysis with Lisa. |
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Binned motif-enrichment analysisBin regions of interest and analyse motifs enrichments in bins. |
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Bin elements of |
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Get and set the zero bin manually |
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Binned Motif Enrichment Analysis with |
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Prepare and run HOMER motif enrichment analysis. |
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Plot diagnostics of binned sequences |
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Density plot of binned elements. |
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Histogram of binned elements. |
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Scatter plot (xy-plot) of binned elements. |
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Heatmap of motif enrichments. |
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K-mer analysisFunctions for analysing word (k-mer) occurrences in sequences. |
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Calculate observed and expected k-mer frequencies |
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Calculate k-mer enrichment in bins of sequences. |
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Identify predictive motifs using stability selectionFunctions for selecting motifs that explain observed changes using Stability Selection. |
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Randomized Lasso Stability Selection |
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Plot selection probabilities of predictors |
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Plot Stability Paths |
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MiscellaneousVarious utilites and helper functions, typically used in the functions above. |
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Find motif matches in sequences. |
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Sequence logo annotation |
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Dump Jaspar motifs into a HOMER motif file. |
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Read a HOMER motif file and create a PFMatrixList |
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Find HOMER script file. |
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Prepare input files for HOMER motif enrichment analysis. |
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load output from HOMER findMotifsGenome.pl into R |
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Calculate similarities between pairs of motifs. |
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Calculate similarities between motifs and k-mers. |
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Create a simple sequence logo grob. |
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Get colors by bin. |
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Sample random regions of fixed length. |