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Fan Chen committed May 6, 2021
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# SURF

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## Installation

<!-- You can install the released version of `surf` from [CRAN](https://CRAN.R-project.org) with: -->

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<!-- install.packages("surf") -->

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You can install the development version of `surf` from
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SURF is versatile in handling ATR event-centric analysis. Provided the
data, here are four different things you could do with SURF.

| | Data | Format | Task |
| :-: | ------------------- | :---------------: | ------------------------------------- |
| 1 | genome annotation | any (gtf, gff, …) | parse ATR events |
| 2 | \+ RNA-seq | alignment (bam) | detect differential ATR events |
| 3 | \+ CLIP-seq | alignment (bam) | detect functional association |
| 4 | \+ external RNA-seq | summarized table | differential transcriptional activity |
| | Data | Format | Task |
|:---:|---------------------|:-----------------:|---------------------------------------|
| 1 | genome annotation | any (gtf, gff, …) | parse ATR events |
| 2 | \+ RNA-seq | alignment (bam) | detect differential ATR events |
| 3 | \+ CLIP-seq | alignment (bam) | detect functional association |
| 4 | \+ external RNA-seq | summarized table | differential transcriptional activity |

## SURF Pipeline

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