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pancanatlas_code_public

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Public repository containing research code for the TCGA PanCanAtlas Splicing project

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# Code for *Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients*
Public repository containing research code for the TCGA PanCanAtlas Splicing project accompanying
the manuscript *Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients*

The code is organized in several sub-directories, which contain the following content:

* **`alt_splice`** 
Code concerning the detection and analysis of alternative splicing events.

* **`events`**  
    Wrapper code for the detection of splicing events in the cohort using SplAdder.

* **`event_stats`**  
    Code for visualising the event type distributions and number of alternative splicing events detected
    per cancer type.

* **`filtering`**  
    Code implementing various filters on the AS events, based on read coverage, min delta PSI, etc.
    
    * **`complexity`**  
    Detection of neo-junctions predominantly present in cancer samples but absent from annotation or the GTEx outgroup.

* **`splice_outliers`**  
    Code for detection and visualization of splicing outliers.

* **`tumor_vs_normal_rank`**  
    Identification and ranking of tumor specific introns.

* **`tumor_vs_normal_stats`**  
    Assessment of events detected in tumor samples vs normal samples.

* **`tumor_vs_normal_test`**  
    Differential testing of tumor vs normal samples on sets of subsamples per cancer type.

* **`neoepitopes`**  
Contains code for the visualization of results on the prediction of neo-epitopes.

* **`peptide_generation`**  
Code concerned with generating peptides from splice-graphs.

* **`qc`**  
Code and additional resources related to quality control of input data.

* **`sample_processing_rna`**  
Code for pre-processing and alignment of the RNA-Seq data, including expression counting, the
collection of usage statistics, and construction of splicing graphs.

* **`sqtl`**  
Visualization scripts for the sQTL analyses.

* **`tSNE_and_heatmap_visualizations`**  
Code for tSNE embeddings on alternative splicing and expression data as well as scripts 
for visualization and different highlightings.

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