_pkgdown.yml

destination: docs
reference:
  - title: "Data: Classes"
    desc: >
      Classes for managing the data from one or more cytometry datasets (FCS files).
    contents:
      - flowFrame-class
      - flowSet-class
      - coerce
      - flowSet_to_list
  - title: "Data: Methods"
    desc: >
      Methods for accessing the data and metadata associated with flowFrame or flowSet objects.
    contents:
      - Subset-methods
      - each_col
      - fr_append_cols
      - getIndexSort-methods
      - fsApply
      - identifier
      - markernames
      - getChannelMarker
      - parameters-methods
      - keyword-methods
  - title: "Reading/writing data"
    desc: >
      Methods for reading/writing cytometry data and metadata from FCS files to/from flowCore data structures.
    contents:
      - read.FCS
      - read.FCSheader
      - read.flowSet
      - collapse_desc
      - write.FCS
      - write.flowSet
  - title: "Compensation"
    desc: >
      Classes to represent compensation to be applied to raw cytometry data and methods to apply them.
    contents:
      - compensation-class
      - decompensate-methods
      - compensatedParameter-class
  - title: "Filters: Classes"
    desc: >
      Classes representing general filters applied to cytometry data and methods to create them.
    contents:
      - filter-class
      - concreteFilter-class
      - transformFilter-class
      - expressionFilter-class
      - parameterFilter-class
      - filterList-class
      - filters-class
      - filtersList-class
      - filterResult-class
      - filterResultList-class
      - filterSummary-class
      - filterSummaryList-class
      - filterReference-class
      - filterDetails
      - timeFilter-class
      - boundaryFilter-class
      - kmeansFilter-class
      - unionFilter-class
      - intersectFilter-class
      - complementFilter-class
      - subsetFilter-class
      - setOperationFilter-class
      - sampleFilter-class
      - logicalFilterResult-class
      - randomFilterResult-class
      - manyFilterResult-class
  - title: "Filters: Methods"
    desc: >
      Methods for applying filters, accessing information about them, and logically combining them.
    contents:
      - '%&%'
      - '%in%'
      - '%on%'
      - filter-methods
      - split-methods
      - summarizeFilter-methods
  - title: "Gates: Classes"
    desc: >
      Classes representing geometric gates (which are themselves filter objects).
      Note that gates are applied to data in the same way as other filters.
    contents:
      - rectangleGate-class
      - quadGate-class
      - polygonGate-class
      - polytopeGate-class
      - ellipsoidGate-class
  - title: "Gates: Methods"
    desc: >
      Methods for applying simple geometric manipulations to gates.
    contents:
      - transform_gate
      - scale_gate
      - shift_gate
      - rotate_gate
  - title: "Transformations"
    desc: >
      Classes for representing transformations to be applied to cytometry data in analysis
      and methods for generating them, interacting with them, and applying them.
    contents:
      - transform
      - transform-class
      - transformList-class
      - transformMap-class
      - transformReference-class
      - parameterTransform-class
      - unitytransform-class
      - scaleTransform
      - truncateTransform
      - dg1polynomial-class
      - ratio-class
      - ratiotGml2-class
      - linearTransform
      - lintGml2-class
      - squareroot-class
      - quadratic-class
      - quadraticTransform
      - exponential-class
      - logarithm-class
      - logTransform
      - logtGml2-class
      - hyperlog-class
      - hyperlogtGml2-class
      - lnTransform
      - splitscale-class
      - splitScaleTransform
      - invsplitscale-class
      - sinht-class
      - asinht-class
      - arcsinhTransform
      - asinhtGml2-class
      - biexponentialTransform
      - EHtrans-class
      - logicleTransform
      - FCSTransTransform
      - logicletGml2-class
      - estimateMedianLogicle
      - inverseLogicleTransform
      - normalization-class
  - title: "Data"
    desc: >
      Datasets included for use in examples to illustrate flowCore functionality
    contents:
      - GvHD
navbar:
  title: flowCore
  right:
    - icon: fas fa fa-github fa-lg
      href: https://github.com/RGLab/flowCore
articles:
  - title: Introduction
    contents:
      - HowTo-flowCore