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Update README.md #5

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32 changes: 19 additions & 13 deletions README.md
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Expand Up @@ -44,25 +44,31 @@ Gregoricchio S. *et al.*, *Nucleic Acids Research* (2022)


## Dependencies/Requirements
### Bioconductor libraries
### Unavailble libraries
Some functions require packages that are noy available anymore on Bioconductor (namely `SUSHI` and `diffloop`).
These can be installed (in the following order) as indicated below:

Some functions of this package require `Bioconductor` libraries. These functions should install automatically with the package.
However, if you prefer to manually install `Bioconductor` and required packages proceed with the `Bioconductor` installation:
```r
# Install devtools from CRAN
install.packages("devtools")

# Or the development version from GitHub:
## install.packages("devtools")
## devtools::install_github("r-lib/devtools")

# Install SUSHI package
devtools::install_github("https://github.com/PhanstielLab/Sushi",
build_manual = FALSE,
build_vignettes = FALSE)

```r
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install()
# Install diffloop package
devtools::install_github("https://github.com/aryeelab/diffloop",
build_manual = FALSE,
build_vignettes = FALSE)
```

The required Biocondutor packages are: `Biostrings`, `biomaRt`, `diffloop`, `GO.db`, `rtracklayer`, `GenomicRanges`, `AnnotationFilter`, `EnsDb.Hsapiens.v75`, `EnsDb.Hsapiens.v86`, `EnsDb.Mmusculus.v79`.
To install it manually proceed with:


```r
BiocManager::install(c("Biostrings", "biomaRt", "diffloop", "GO.db", "rtracklayer", "GenomicRanges", "AnnotationFilter", "EnsDb.Hsapiens.v75", "EnsDb.Hsapiens.v86", "EnsDb.Mmusculus.v79"))
```
<br />

### deepTools
Expand All @@ -85,7 +91,7 @@ Certain functions of this package require that `bedtools` is installed on your s

<br />

## Installation
## Installation of `Rseb`
```r
# Install devtools from CRAN
install.packages("devtools")
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