Merge pull request #80 from shahcompbio/develop

Update README with release links

README.md

@@ -2,7 +2,7 @@
 
 This repository contains supporting material for the manuscript:
 
-> "Ovarian cancer mutational processes drive site-specific immune evasion"
+> I. Vázquez-García, F. Uhlitz et al, ["Ovarian cancer mutational processes drive site-specific immune evasion"](https://www.nature.com/articles/s41586-022-05496-1), *Nature* (2022)
 
 ## Table of Contents
 
@@ -24,7 +24,7 @@ The source code contains RMarkdown notebooks to reproduce the manuscript figures
 
 ### Overview
 
-The MSK SPECTRUM study is registered on dbGaP under accession number [phs002857.v1.p1](https://www.ncbi.nlm.nih.gov/projects/gapprev/gap/cgi-bin/study.cgi?study_id=phs002857.v1.p1).
+The MSK SPECTRUM study is registered on dbGaP under accession number [phs002857.v1.p1](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002857.v1.p1).
 
 A Synapse page for the MSK SPECTRUM study is available to provide access to multi-modal datasets from one central location. This page can be accessed under accession number [syn25569736](https://www.synapse.org/msk_spectrum).
 
@@ -44,9 +44,9 @@ A Synapse page for the MSK SPECTRUM study is available to provide access to mult
   - Somatic mutations, copy number and structural variants can be visualized through [cBioPortal](https://cbioportal.org/study/summary?id=msk_spectrum_tme_2022).
 
 #### H&E
-  - Deidentified images are available via [dbGaP](https://www.ncbi.nlm.nih.gov/projects/gapprev/gap/cgi-bin/study.cgi?study_id=phs002857.v1.p1).
+  - Deidentified images are available via [dbGaP](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002857.v1.p1).
   - Cell segmentation, tissue segmentation and lymphocyte classification are available from [Synapse](https://www.synapse.org/#!Synapse:syn33521762/datasets/).
 
 #### mpIF
-  - Deidentified images are available via [dbGaP](https://www.ncbi.nlm.nih.gov/projects/gapprev/gap/cgi-bin/study.cgi?study_id=phs002857.v1.p1).
+  - Deidentified images are available via [dbGaP](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002857.v1.p1).
   - Cell segmentation, tissue segmentation and cell phenotyping are available from [Synapse](https://www.synapse.org/#!Synapse:syn33520881/datasets/).