package bistro-bio

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type 'a signal_format
type 'a img_format
val bamcoverage : ?scalefactor:float -> ?filterrnastrand:[ `forward | `reverse ] -> ?binsize:int -> ?blacklist:Formats.bed3 Bistro.file -> ?threads:int -> ?normalizeUsing:[ `RPKM | `CPM | `BPM | `RPGC ] -> ?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.directory -> 'a Bistro.file
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:Formats.bed3 Bistro.file -> ?threads:int -> ?normalizeUsing:[ `RPKM | `CPM | `BPM | `RPGC ] -> ?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.directory -> [ `indexed_bam ] Bistro.directory -> 'a Bistro.file
val bigwigcompare : ?scalefactor:float -> ?ratio: [ `log2 | `ratio | `subtract | `add | `mean | `reciprocal_ratio | `first | `second ] -> ?pseudocount:int -> ?binsize:int -> ?region:string -> ?blacklist:Formats.bed3 Bistro.file -> ?threads:int -> 'a signal_format -> Ucsc_gb.bigWig Bistro.file -> Ucsc_gb.bigWig Bistro.file -> 'a Bistro.file
class type compressed_numpy_array = object ... end
val multibamsummary_bins : ?binsize:int -> ?distancebetweenbins:int -> ?region:string -> ?blacklist:Formats.bed3 Bistro.file -> ?threads:int -> ?outrawcounts:bool -> ?extendreads:int -> ?ignoreduplicates:bool -> ?minmappingquality:int -> ?centerreads:bool -> ?samflaginclude:int -> ?samflagexclude:int -> ?minfragmentlength:int -> ?maxfragmentlength:int -> [ `indexed_bam ] Bistro.directory list -> compressed_numpy_array Bistro.file
val multibamsummary_bed : ?region:string -> ?blacklist:Formats.bed3 Bistro.file -> ?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 -> Formats.bed3 Bistro.file -> [ `indexed_bam ] Bistro.directory list -> compressed_numpy_array Bistro.file
val multibigwigsummary_bed : ?labels:string list -> ?chromosomesToSkip:string list -> ?region:string -> ?blacklist:Formats.bed3 Bistro.file -> ?threads:int -> ?metagene:bool -> ?transcriptid:bool -> ?exonid:bool -> ?transcriptiddesignator:bool -> Formats.bed3 Bistro.file -> Ucsc_gb.bigWig Bistro.file list -> compressed_numpy_array Bistro.file * Bistro.tsv Bistro.file
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:Formats.bed3 Bistro.file -> ?scale:float -> ?numberOfProcessors:int -> regions:Formats.bed3 Bistro.file list -> scores:Ucsc_gb.bigWig Bistro.file list -> unit -> deeptools_matrix Bistro.gz Bistro.file
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.gz Bistro.file -> 'a Bistro.file
val plotCorrelation : ?skipZeros:bool -> ?labels:string list -> ?plotTitle:string -> ?removeOutliers:bool -> ?colorMap:string -> ?plotNumbers:bool -> ?log1p:bool -> corMethod:[ `spearman | `pearson ] -> whatToPlot:[ `heatmap | `scatterplot ] -> 'a img_format -> compressed_numpy_array Bistro.file -> 'a Bistro.file
val plotProfile : ?dpi:int -> ?kmeans:int -> ?hclust:int -> ?averageType:[ `mean | `median | `min | `max | `std | `sum ] -> ?plotHeight:float -> ?plotWidth:float -> ?plotType:[ `lines | `fill | `se | `std | `overlapped_lines | `heatmap ] -> ?colors:string list -> ?numPlotsPerRow:int -> ?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.gz Bistro.file -> 'a Bistro.file

plotHeight and plotWidth are given in cm

val plotEnrichment : ?labels:string list -> ?regionLabels:string list -> ?plotTitle:string -> ?variableScales:bool -> ?plotHeight:float -> ?plotWidth:float -> ?colors:string list -> ?numPlotsPerRow:int -> ?alpha:float -> ?offset:int -> ?blackList:Formats.bed3 Bistro.file -> ?numberOfProcessors:int -> bams:Formats.bam Bistro.file list -> beds:Formats.bed3 Bistro.file list -> 'a img_format -> 'a Bistro.file
val plotFingerprint : ?extendReads:bool -> ?ignoreDuplicates:bool -> ?minMappingQuality:int -> ?centerReads:bool -> ?samFlagInclude:int -> ?samFlagExclude:int -> ?minFragmentLength:int -> ?maxFragmentLength:int -> ?labels:string list -> ?binSize:int -> ?numberOfSamples:int -> ?plotTitle:string -> ?skipZeros:bool -> ?region:string -> ?blackList:Formats.bed3 Bistro.file -> ?numberOfProcessors:int -> 'a img_format -> [ `indexed_bam ] Bistro.directory list -> 'a Bistro.file
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