Science Score: 57.0%
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Repository
FRASER - Find RAre Splicing Events in RNA-seq
Basic Info
Statistics
- Stars: 47
- Watchers: 6
- Forks: 24
- Open Issues: 29
- Releases: 15
Topics
Metadata Files
README.md
FRASER - Find RAre Splicing Events in RNA-seq
FRASER is a tool to detect aberrant splicing events in RNA-seq data. The method is described and published in Nature Communications and available through Bioconductor. It is also part of the Detection of RNA Outlier Pipeline (DROP). DROP is described and published in Nature Protocols.
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 or our Colab tutorial at: 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 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
In version 2.4.5, we fixed a bug affecting unstranded paired-end data. We were counting read fragments instead of read pairs. The counted split reads with the fixed method are, on average, lower by around 20%. If you have such data, please rerun your entire analysis from the start (make sure you have recount=TRUE).
In version 2.4.3, instead of doing a grid search to determine the optimal encoding dimension of the denoising autoencoder, we now use the Optimal Hard Threshold (OHT). This makes the algorithm 6-10 times faster!
⚠️ Also, since this version, FRASER is released under CC-BY-NC 4.0, meaning it requires a license for any commercial use. If you want to use it for commercial purposes, please contact us.
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 pseudocounts, filtering settings and default delta cutoff.
To change the splice metric, set fitMetrics(fds) to one or more of the metrics
specified in FRASER::psiTypes. For FRASER 2.0 and the Intron Jaccard Index, the
new default delta cutoff is 0.1 instead of the previous value of 0.3. When using
the 3 previous metrics, the delta cutoff should be set manually to 0.3
during results extraction, e.g. results(fds, deltaPsiCutoff=0.3,...).
Installation
FRASER is an R/Bioconductor software package requiring a running
R 3.6 version or higher.
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 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
or MacOS X).
``` if (!requireNamespace("devtools", quietly=TRUE)) install.packages('devtools')
latest development version
devtools::install_github('gagneurlab/FRASER', dependencies=TRUE)
or a specific version of FRASER (search for tags on github)
devtools::install_github('gagneurlab/FRASER', ref='1.1.3', dependencies=TRUE) ```
If you have dependency issues while installing any package, please have a look at the Troubleshooting section or submit an issue on GitHub.
Troubleshooting
Error in UseMethod("filter_")
When using FRASER with R3.6 one might observe the following error:
``` fds <- annotateRanges(fds)
Error in UseMethod("filter_") :
no applicable method for 'filter' applied to an object of class "c('tblSQLiteConnection', 'tbldbi', 'tblsql', 'tbl_lazy', 'tbl')"
```
To overcome this error one needs to upgrade BiocFileCache.
BiocManager::install("Bioconductor/BiocFileCache", ask=FALSE, update=FALSE)
Missing libraries while compiling R packages
On some Linux distributions, we need the developer libraries for compiling the R packages.
To install those packages, please run as administrator:
For Ubuntu or Debian-based systems:
sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev zlib1g-dev libmysqld-dev
For centOS or RHEL based systems:
sudo yum install R-devel zlib-devel openssl-devel libcurl-devel libxml2-devel mariadb-devel
Owner
- Name: Gagneur lab
- Login: gagneurlab
- Kind: organization
- Website: www.gagneurlab.in.tum.de
- Repositories: 18
- Profile: https://github.com/gagneurlab
To understand the genetic basis of gene regulation and its implication in diseases.
GitHub Events
Total
- Create event: 15
- Release event: 4
- Issues event: 14
- Watch event: 8
- Delete event: 9
- Issue comment event: 21
- Push event: 42
- Pull request review event: 5
- Pull request event: 11
- Fork event: 2
Last Year
- Create event: 15
- Release event: 4
- Issues event: 14
- Watch event: 8
- Delete event: 9
- Issue comment event: 21
- Push event: 42
- Pull request review event: 5
- Pull request event: 11
- Fork event: 2
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Christian Mertes | m****s@i****e | 604 |
| Ines Scheller | s****r@i****e | 343 |
| Nitesh Turaga | n****a@g****m | 10 |
| Vicente Yepez | 3****8 | 8 |
| Yingjiqiong Liang | l****i@i****e | 4 |
| Michaela Müller | m****e@i****e | 3 |
| AtaJadidAhari | a****i@g****m | 3 |
| Felix Brechtmann | b****a@i****e | 2 |
| J Wokaty | j****y@s****u | 2 |
| Luise Schuller | l****r@t****e | 2 |
| nickhsmith | s****h@g****m | 2 |
| Vicente | y****z@i****e | 2 |
| Ines Scheller | i****r@i****e | 2 |
| Darío Hereñú | m****a@g****m | 1 |
| Smith Nicholas | s****h@i****e | 1 |
| Salazar Daniela Soraya Andrade | s****r@i****e | 1 |
| Rothammer Sophie Maria | r****s@o****e | 1 |
| Christian Mertes | m****s@b****n | 1 |
| Drew Behrens | d****h@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 39
- Total pull requests: 14
- Average time to close issues: 12 months
- Average time to close pull requests: 13 days
- Total issue authors: 24
- Total pull request authors: 5
- Average comments per issue: 1.69
- Average comments per pull request: 0.36
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 9
- Pull requests: 13
- Average time to close issues: about 2 months
- Average time to close pull requests: 14 days
- Issue authors: 8
- Pull request authors: 5
- Average comments per issue: 0.78
- Average comments per pull request: 0.31
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- fburdet (5)
- deb0612 (3)
- qj009 (2)
- jialanm (2)
- Hoeze (2)
- Wynandi (2)
- tlz4320 (2)
- lyj95618 (2)
- h-joshi (2)
- dkhalenkw (2)
- mmartinezj (2)
- lemdcock (1)
- Vinniporiya (1)
- MiqG (1)
- mincej (1)
Pull Request Authors
- AtaJadidAhari (7)
- c-mertes (4)
- andrearaithel (2)
- Copilot (1)
- vyepez88 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 14,141 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 8
- Total maintainers: 1
bioconductor.org: FRASER
Find RAre Splicing Events in RNA-Seq Data
- Homepage: https://github.com/gagneurlab/FRASER
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/FRASER/inst/doc/FRASER.pdf
- License: file LICENSE
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Latest release: 2.4.3
published 8 months ago
Rankings
Maintainers (1)
Dependencies
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