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_pkgdown.yml
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/
_pkgdown.yml
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url: https://grandr.erhard-lab.de
template:
bootstrap: 5
bootswatch: flatly
lang: en
search:
exclude: ['.github/issue_template.md']
navbar:
title: "grandR"
left:
- text: "Getting started"
href: articles/getting-started.html
- text: "Walk-throughs"
menu:
- text: "Differential expression (snapshot data)"
href: articles/web/differential-expression.html
- text: "Kinetic modeling (progressive labeling time courses)"
href: articles/web/kinetic-modeling.html
- text: "Learn more"
menu:
- text: "Loading data and working with grandR objects"
href: articles/web/loading-data.html
- text: "Working with data matrices and analysis results"
href: articles/web/data-matrices-and-analysis-results.html
- text: "Plotting & web-interface"
href: articles/web/plotting.html
- text: "Fitting pulse-chase data"
href: articles/web/pulse-chase.html
- text: "Single cell data analysis"
href: articles/web/single-cell.html
- text: "Detecting and correcting 4sU dropout"
href: articles/web/4sU-dropout.html
- text: Discussions
href: "https://github.com/erhard-lab/grandR/discussions"
- text: "News"
href: news/index.html
- text: "Reference"
href: reference/index.html
right:
- icon: fa-home
href: ../
- icon: fa-github
href: https://github.com/erhard-lab/grandR
reference:
- title: Fundamentals
- subtitle: Loading data
desc: Functions to read data from files or urls
- contents:
- has_concept("load")
- subtitle: Data preprocessing
desc: Functions to preprocess data
- contents:
- has_concept("preprocess")
- subtitle: Interacting with grandR objects
desc: Retrieve information from grandR objects
- contents:
- has_concept("grandr")
- subtitle: Data retrieval
desc: Functions and helper functions to retrieve data from grandR objects
- contents:
- has_concept("data")
- title: Analyses
- subtitle: Differential expression
desc: Analyze differential expression (snapshot experiments)
- contents:
- has_concept("diffexp")
- subtitle: Progressive labeling timecourses
desc: Infer kinetic parameters from progressive labeling timecourses
- contents:
- has_concept("kinetics")
- subtitle: Modeling snapshot data
desc: Infer parameters from snapshot data with or without steady state assumptions
- contents:
- has_concept("snapshot")
- subtitle: Gene set tests
desc: Functions to do GSEA,ORA,etc.
- contents:
- has_concept("genesets")
- title: Visualization
- subtitle: Gene plots
desc: Functions to plot data for a single gene
- contents:
- has_concept("geneplot")
- subtitle: Global plots
desc: Functions to plot data summarizing the whole data set
- contents:
- has_concept("globalplot")
- subtitle: Web interface
desc: Functions related to the shiny web-interface
- contents:
- has_concept("shiny")
- title: QC
- subtitle: 4sU dropout checks
desc: Functions to check for 4sU dropout
- contents:
- has_concept("dropout")
- subtitle: Temporal recalibration
desc: Functions for recalibration of labeling times (to get effective labeling from nominal labeling times)
- contents:
- has_concept("recalibration")
- subtitle: GRAND3 quality control plots
desc: Generate quality control plot from the statistics generated by GRAND3
- contents:
- has_concept("diagnostics")
- title: Misc
- subtitle: Read simulation
desc: Functions for in-silico simulation of nucleotide conversion data
- contents:
- has_concept("simulation")
- subtitle: Helper functions
desc:
- contents:
- has_concept("helper")