url: https://thelovelab.github.io/fishpond

title: fishpond

authors:
  Anqi Zhu:
    href: https://www.linkedin.com/in/aqzhu91
  Michael Love:
    href: https://mikelove.github.io
  Avi Srivastava:
    href: https://k3yavi.github.io
  Rob Patro:
    href: https://combine-lab.github.io
  Joseph Ibrahim:
    href: https://sph.unc.edu/adv_profile/joseph-g-ibrahim-phd
  Hirak Sarkar:
    href: https://hiraksarkar.github.io
  Euphy Wu:
    href: https://www.linkedin.com/in/euphy-wu-09b14383
  Noor Pratap Singh:
    href: https://combine-lab.github.io/members/noor-pratap-singh.html
  Scott Van Buren:
    href: https://www.linkedin.com/in/scottvanburen
  Dongze He:
    href: https://combine-lab.github.io/members/dongze-he.html
  Steve Lianoglou:
    href: https://www.linkedin.com/in/slianoglou
  Wes Wilson:
    href: https://www.med.upenn.edu/albeldalab/wes-wilson.html
  Jeroen Gilis:
    href: https://be.linkedin.com/in/jeroen-gilis-4044b5151

figures:
  fig.width: 5.5
  fig.retina: 1

articles:
  - title: Swish
    navbar: ~
    contents:
      - swish
      - allelic

reference:
  - title: Fishpond
  - contents:
    - fishpond-package
  - title: Swish method
  - contents:
    - scaleInfReps
    - labelKeep
    - swish
  - title: Main Swish plotting functions
  - contents:
    - plotInfReps
    - plotMASwish
  - title: Helper functions
  - contents:
    - computeInfRV
    - getTrace
    - isoformProportions
    - makeSimSwishData
  - title: Import and utilities
  - contents:
    - loadFry
    - alevinEC
    - salmonEC
  - title: Allelic analysis and plotting
  - contents:
    - importAllelicCounts
    - makeTx2Tss    
    - plotAllelicGene
    - plotAllelicHeatmap
  - title: Compression
  - contents:
    - splitSwish
    - addStatsFromCSV
    - makeInfReps
    - miniSwish
  - title: Experimental
  - contents:
    - deswish
