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Re-build README.Rmd
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mcanouil committed Nov 24, 2022
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Expand Up @@ -49,25 +49,25 @@ an interactive web application.
With the use of two functions, RCC files are summarised and visualised,
namely: `load_rcc()` and `visualise()`.

- The `load_rcc()` function is used to preprocess the data.
- The `visualise()` function initiates a [Shiny-based
dashboard](https://shiny.rstudio.com/) that visualises all relevant
QC plots.
- The `load_rcc()` function is used to preprocess the data.
- The `visualise()` function initiates a [Shiny-based
dashboard](https://shiny.rstudio.com/) that visualises all relevant QC
plots.

*NACHO* also includes a function `normalise()`, which (re)calculates
sample specific size factors and normalises the data.

- The `normalise()` function creates a list in which your settings,
the raw counts and normalised counts are stored.
- The `normalise()` function creates a list in which your settings, the
raw counts and normalised counts are stored.

In addition (since v0.6.0) *NACHO* includes two (three) additional
functions:

- The `render()` function renders a full quality-control report (HTML)
based on the results of a call to `load_rcc()` or `normalise()`
(using `print()` in a Rmarkdown chunk).
- The `autoplot()` function draws any quality-control metrics from
`visualise()` and `render()`.
- The `render()` function renders a full quality-control report (HTML)
based on the results of a call to `load_rcc()` or `normalise()` (using
`print()` in a Rmarkdown chunk).
- The `autoplot()` function draws any quality-control metrics from
`visualise()` and `render()`.

For more `vignette("NACHO")` and `vignette("NACHO-analysis")`.

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