bistro-bio 0.6.0 (latest) · OCaml Package

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.png img_format

val pdf : Bistro.pdf img_format

val svg : Bistro.svg 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

package bistro-bio