@@ -42,7 +42,7 @@ your home directory: `~/ICoVeR/`.
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@@ -42,7 +42,7 @@ your home directory: `~/ICoVeR/`.
## Quick start
## Quick start
The easiest way to get started with ICoVeR is by installing the package with the pre-loaded CSTR data set.
The easiest way to get started with ICoVeR is by installing the package with the pre-loaded CSTR data set.
The CSTR data set is generated by us from and consists of multiple samples from an anaerobic digester.
The CSTR data set is generated by us and consists of multiple samples from an anaerobic digester.
This data is already in the repository under [R.ICoVeR/data](https://github.com/bbroeksema/ICoVeR/tree/master/R.ICoVeR/data).
This data is already in the repository under [R.ICoVeR/data](https://github.com/bbroeksema/ICoVeR/tree/master/R.ICoVeR/data).
To install ICoVeR open [R.ICoVeR/ICoVeR.Rproj](https://github.com/bbroeksema/ICoVeR/blob/master/R.ICoVeR/ICoVeR.Rproj) in RStudio and use the "build and reload" button in the build tab (top right of the screen).
To install ICoVeR open [R.ICoVeR/ICoVeR.Rproj](https://github.com/bbroeksema/ICoVeR/blob/master/R.ICoVeR/ICoVeR.Rproj) in RStudio and use the "build and reload" button in the build tab (top right of the screen).
Alternatively. use an R-session to install the ICoVeR package:
Alternatively. use an R-session to install the ICoVeR package:
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@@ -78,13 +78,13 @@ To prepare the data files read by ICoVer you have to provide the following files
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@@ -78,13 +78,13 @@ To prepare the data files read by ICoVer you have to provide the following files
*[REQ] An [essential single copy gene file](https://github.com/bbroeksema/ICoVeR/blob/master/data/wrighton_escg.csv) with contig - gene pairs
*[REQ] An [essential single copy gene file](https://github.com/bbroeksema/ICoVeR/blob/master/data/wrighton_escg.csv) with contig - gene pairs
*[OPT] A [clusterings file](https://github.com/bbroeksema/ICoVeR/blob/master/data/wrighton_clusterings.csv) with binning results from one or more automated binning tools such as metabat. Although optional, it is highly recommended to start with an automated approach to speed up the verification and refinement process.
*[OPT] A [clusterings file](https://github.com/bbroeksema/ICoVeR/blob/master/data/wrighton_clusterings.csv) with binning results from one or more automated binning tools such as metabat. Although optional, it is highly recommended to start with an automated approach to speed up the verification and refinement process.
**TODO: ** Add some notes on what tools we used to create those files.
<!-- **TODO: ** Add some notes on what tools we used to create those files. -->
## Preprocessing
## Preprocessing
In order to load the data into our interactive contig binning system, we need to pre-process the afore mentioned files.
In order to load the data into our interactive contig binning system, we need to pre-process the afore mentioned files.
This is done by using the scripts provided in the R.preprocessing directory.
This is done by using the scripts provided in the R.preprocessing directory.
In this example we will prepare the wrighton data set for ICoVeR.
In this example we will prepare the Wrighton data set for ICoVeR.
The `PrepareDataForInteractiveBinning` function performs the following steps:
The `PrepareDataForInteractiveBinning` function performs the following steps: