Module Bistro_bioinfo.Deeptools

type 'a signal_format
val bigwig : Ucsc_gb.bigWig signal_format
val bedgraph : Ucsc_gb.bedGraph signal_format
type 'a img_format
val png : Bistro.Std.png img_format
val pdf : Bistro.Std.pdf img_format
val svg : Bistro.Std.svg img_format
val bamcoverage : ?⁠scalefactor:float ‑> ?⁠filterrnastrand:[ `forward | `reverse ] ‑> ?⁠binsize:int ‑> ?⁠blacklist:Bistro_bioinfo.Defs.#bed3 Bistro.Std.workflow ‑> ?⁠threads:int ‑> ?⁠normalizeto1x:int ‑> ?⁠normalizeusingrpkm:bool ‑> ?⁠ignorefornormalization:string list ‑> ?⁠skipnoncoveredregions:bool ‑> ?⁠smoothlength:int ‑> ?⁠extendreads:int ‑> ?⁠ignoreduplicates:bool ‑> ?⁠minmappingquality:int ‑> ?⁠centerreads:bool ‑> ?⁠samflaginclude:int ‑> ?⁠samflagexclude:int ‑> ?⁠minfragmentlength:int ‑> ?⁠maxfragmentlength:int ‑> 'a signal_format ‑> [ `indexed_bam ] Bistro.Std.directory Bistro.Std.workflow ‑> 'a Bistro.Std.workflow
val bamcompare : ?⁠scalefactormethod:[ `readcount | `ses ] ‑> ?⁠samplelength:int ‑> ?⁠numberofsamples:int ‑> ?⁠scalefactor:float ‑> ?⁠ratio:[ `log2 | `ratio | `subtract | `add | `mean | `reciprocal_ratio | `first | `second ] ‑> ?⁠pseudocount:int ‑> ?⁠binsize:int ‑> ?⁠region:string ‑> ?⁠blacklist:Bistro_bioinfo.Defs.#bed3 Bistro.Std.workflow ‑> ?⁠threads:int ‑> ?⁠normalizeto1x:int ‑> ?⁠normalizeusingrpkm:bool ‑> ?⁠ignorefornormalization:string list ‑> ?⁠skipnoncoveredregions:bool ‑> ?⁠smoothlength:int ‑> ?⁠extendreads:int ‑> ?⁠ignoreduplicates:bool ‑> ?⁠minmappingquality:int ‑> ?⁠centerreads:bool ‑> ?⁠samflaginclude:int ‑> ?⁠samflagexclude:int ‑> ?⁠minfragmentlength:int ‑> ?⁠maxfragmentlength:int ‑> 'a signal_format ‑> [ `indexed_bam ] Bistro.Std.directory Bistro.Std.workflow ‑> [ `indexed_bam ] Bistro.Std.directory Bistro.Std.workflow ‑> 'a Bistro.Std.workflow
val bigwigcompare : ?⁠scalefactor:float ‑> ?⁠ratio:[ `log2 | `ratio | `subtract | `add | `mean | `reciprocal_ratio | `first | `second ] ‑> ?⁠pseudocount:int ‑> ?⁠binsize:int ‑> ?⁠region:string ‑> ?⁠blacklist:Bistro_bioinfo.Defs.#bed3 Bistro.Std.workflow ‑> ?⁠threads:int ‑> 'a signal_format ‑> Ucsc_gb.bigWig Bistro.Std.workflow ‑> Ucsc_gb.bigWig Bistro.Std.workflow ‑> 'a Bistro.Std.workflow
class type compressed_numpy_array = object ... end
val multibamsummary_bins : ?⁠binsize:int ‑> ?⁠distancebetweenbins:int ‑> ?⁠region:string ‑> ?⁠blacklist:Bistro_bioinfo.Defs.#bed3 Bistro.Std.workflow ‑> ?⁠threads:int ‑> ?⁠outrawcounts:bool ‑> ?⁠extendreads:int ‑> ?⁠ignoreduplicates:bool ‑> ?⁠minmappingquality:int ‑> ?⁠centerreads:bool ‑> ?⁠samflaginclude:int ‑> ?⁠samflagexclude:int ‑> ?⁠minfragmentlength:int ‑> ?⁠maxfragmentlength:int ‑> Defs.indexed_bam Bistro.Std.workflow list ‑> compressed_numpy_array Bistro.Std.workflow
val multibamsummary_bed : ?⁠region:string ‑> ?⁠blacklist:Bistro_bioinfo.Defs.#bed3 Bistro.Std.workflow ‑> ?⁠threads:int ‑> ?⁠outrawcounts:bool ‑> ?⁠extendreads:int ‑> ?⁠ignoreduplicates:bool ‑> ?⁠minmappingquality:int ‑> ?⁠centerreads:bool ‑> ?⁠samflaginclude:int ‑> ?⁠samflagexclude:int ‑> ?⁠minfragmentlength:int ‑> ?⁠maxfragmentlength:int ‑> ?⁠metagene:bool ‑> ?⁠transcriptid:bool ‑> ?⁠exonid:bool ‑> ?⁠transcriptiddesignator:bool ‑> Bistro_bioinfo.Defs.#bed3 Bistro.Std.workflow ‑> Defs.indexed_bam Bistro.Std.workflow list ‑> compressed_numpy_array Bistro.Std.workflow
class type deeptools_matrix = object ... end
val computeMatrix_reference_point : ?⁠referencePoint:[ `TSS | `TES | `center ] ‑> ?⁠upstream:int ‑> ?⁠downstream:int ‑> ?⁠nanAfterEnd:bool ‑> ?⁠binSize:int ‑> ?⁠sortRegions:[ `descend | `ascend | `no | `keep ] ‑> ?⁠sortUsing:[ `mean | `median | `max | `min | `sum | `region_length ] ‑> ?⁠sortUsingSamples:int list ‑> ?⁠averageTypeBins:[ `mean | `median | `min | `max | `std | `sum ] ‑> ?⁠missingDataAsZero:bool ‑> ?⁠skipZeros:bool ‑> ?⁠minThreshold:float ‑> ?⁠maxThreshold:float ‑> ?⁠blackList:Bistro_bioinfo.Defs.#bed3 Bistro.Std.workflow ‑> ?⁠scale:float ‑> ?⁠numberOfProcessors:int ‑> regions:Bistro_bioinfo.Defs.#bed3 Bistro.Std.workflow list ‑> scores:Ucsc_gb.bigWig Bistro.Std.workflow list ‑> unit ‑> deeptools_matrix Bistro.Std.gz Bistro.Std.workflow
val plotHeatmap : ?⁠dpi:int ‑> ?⁠kmeans:int ‑> ?⁠hclust:int ‑> ?⁠sortRegions:[ `descend | `ascend | `no ] ‑> ?⁠sortUsing:[ `mean | `median | `max | `min | `sum | `region_length ] ‑> ?⁠sortUsingSamples:int list ‑> ?⁠averageTypeSummaryPlot:[ `mean | `median | `min | `max | `std | `sum ] ‑> ?⁠missingDataColor:string ‑> ?⁠colorMap:string ‑> ?⁠alpha:float ‑> ?⁠colorList:string list ‑> ?⁠colorNumber:int ‑> ?⁠zMin:float list ‑> ?⁠zMax:float list ‑> ?⁠heatmapHeight:float ‑> ?⁠heatmapWidth:float ‑> ?⁠whatToShow:[ `plot_heatmap_and_colorbar | `plot_and_heatmap | `heatmap_only | `heatmap_and_colorbar ] ‑> ?⁠boxAroundHeatmaps:bool ‑> ?⁠xAxisLabel:string ‑> ?⁠startLabel:string ‑> ?⁠endLabel:string ‑> ?⁠refPointLabel:string ‑> ?⁠regionsLabel:string list ‑> ?⁠samplesLabel:string list ‑> ?⁠plotTitle:string ‑> ?⁠yAxisLabel:string ‑> ?⁠yMin:float list ‑> ?⁠yMax:float list ‑> ?⁠legendLocation:[ `best | `upper_right | `upper_left | `upper_center | `lower_left | `lower_right | `lower_center | `center | `center_left | `center_right | `none ] ‑> ?⁠perGroup:bool ‑> 'a img_format ‑> deeptools_matrix Bistro.Std.gz Bistro.Std.workflow ‑> 'a Bistro.Std.workflow