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vyepez88 authored Jun 13, 2024
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Expand Up @@ -9,15 +9,19 @@ FRASER is a tool to detect aberrant splicing events in RNA-seq data. The method

The FRASER framework and workflow aims to assist the diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects. For a short tutorial on how to use FRASER on a dataset please use the [vignette](http://bioconductor.org/packages/release/bioc/vignettes/FRASER/inst/doc/FRASER.pdf) or our Colab tutorial at: [http://tinyurl.com/RNA-ASHG-colab](http://tinyurl.com/RNA-ASHG-colab). The Colab is based on a workshop that we presented at ASHG 2019/2020.

Please cite our method paper if you use it in a publication:
Please cite our method paper FRASER if you use it in a publication:

> Mertes, C., Scheller, I.F., Yépez, V.A. *et al.* Detection of aberrant splicing events in RNA-seq data using FRASER. *Nat Commun* **12**, 529 (2021). https://doi.org/10.1038/s41467-020-20573-7
or if you use FRASER2:

> Scheller, I.F., Lutz, K., Mertes, C *et al.* Improved detection of aberrant splicing with FRASER 2.0 and the intron Jaccard index. *Am Jrnl Hum Genet* **110**, 12 (2023). https://doi.org/10.1016/j.ajhg.2023.10.014
## What's new

FRASER 2.0, an improved version of FRASER, is now available and used by default (version 1.99.0 and above).
FRASER 2.0 uses the Intron Jaccard Index as its splice metric instead of FRASER's
previous three metrics along with some other parameter optimizations of pseudocount,
previous three metrics along with some other parameter optimizations of pseudocounts,
filtering settings and default delta cutoff.

To change the splice metric, set `fitMetrics(fds)` to one or more of the metrics
Expand All @@ -33,14 +37,14 @@ The preprint describing these changes in more detail is available in [medRxiv](h
`FRASER` is an R/Bioconductor software package requiring a running
[R 3.6 version or higher](https://cran.r-project.org/).

The recommanded way of installing `FRASER` is to use `Bioconductor`:
The recommended way of installing `FRASER` is through `Bioconductor`:
```
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages('BiocManager')
BiocManager::install('FRASER')
```

If you use an R version below `4.0.0` you have to install it from source.
If you use an R version below `4.0.0`, you have to install it from the source.
To this end, we will use `devtools` to install it. For this, you need a
working development environment to compile the C++ code (see for
details: [Windows](https://cran.r-project.org/bin/windows/Rtools/)
Expand Down Expand Up @@ -85,7 +89,7 @@ On some Linux distributions we need the developer libraries for compiling the R

To install those packages, please run as administrator:

For Ubuntu or debian based systems:
For Ubuntu or Debian based systems:
```
sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev zlib1g-dev libmysqld-dev
```
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