updated docs and example report DOI

sigven · Jul 13, 2024 · d020e1e · d020e1e
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diff --git a/README.md b/README.md
@@ -1,10 +1,16 @@
 # Cancer Predisposition Sequencing Reporter <a href="https://sigven.github.io/cpsr/"><img src="man/figures/logo.png" align="right" height="118" width="100"/></a>
 
-The *Cancer Predisposition Sequencing Reporter (CPSR)* is a computational workflow that **interprets and classifies the clinical significance of germline DNA variants** identified from next-generation sequencing **in the context of cancer predisposition and inherited cancer syndromes**. The workflow can also report **incidental findings (ACMG v3.2)**.
+The *Cancer Predisposition Sequencing Reporter (CPSR)* is a computational workflow that **interprets DNA sequence variants** identified from next-generation sequencing **in the context of cancer predisposition**. 
 
-The CPSR workflow is integrated with the framework that underlies the [Personal Cancer Genome Reporter - PCGR](https://github.com/sigven/pcgr). While *PCGR* is intended for reporting and analysis of somatic variants detected in a tumor, *CPSR* is intended for reporting and ranking of germline variants in protein-coding genes that are implicated in cancer predisposition and inherited cancer syndromes. 
+*CPSR* accepts a query file with _germline_ variant calls (SNVs/InDels) from a single sample (i.e. cancer patient), encoded in the [VCF format ](https://samtools.github.io/hts-specs/VCFv4.2.pdf). Through comprehensive gene and variant annotation procedures, CPSR offers the following main functionalities to the user:
 
-*CPSR* accepts a query file from a single case/patient, containing raw germline variant calls encoded in the [VCF](https://samtools.github.io/hts-specs/VCFv4.2.pdf) format (i.e. SNVs/InDels). A comprehensive set of **virtual cancer predisposition gene panels** harvested from the [Genomics England PanelApp](https://panelapp.genomicsengland.co.uk/) allows the user to flexibly put a restriction on which genes and findings are displayed in the cancer predisposition report.
+1)  Flexible **selection of cancer predisposition genes** subject to analysis and reporting - through the use of virtual gene panels
+2)  **Variant classification** (*Pathogenic* to *Benign*) through a dedicated implementation of [ACMG/AMP guidelines](https://pubmed.ncbi.nlm.nih.gov/25741868/)
+3)  **Detection of germline biomarkers** - for prognosis, diagnosis, or drug sensitivity/resistance
+4)  Reporting of **secondary/incidental findings** ([ACMG recommendations](https://pubmed.ncbi.nlm.nih.gov/37347242/))
+5)  **Interactive HTML output report** with detailed variant information, gene annotations, and external links to relevant databases
+
+The CPSR workflow is integrated with the framework that underlies the [Personal Cancer Genome Reporter - PCGR](https://github.com/sigven/pcgr). While *PCGR* is intended for reporting and analysis of somatic variants detected in a tumor, *CPSR* is intended for reporting and ranking of germline variants in protein-coding genes that are implicated in cancer predisposition and inherited cancer syndromes.
 
 Snapshots of sections in the [quarto](https://quarto.org)-based cancer predisposition genome report (artificial sample, with more findings than usual) are shown below:
 
@@ -13,44 +19,40 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos
 ## News
 
 -   *July 2024*: **2.0.1 release**
-    - patch with bug fix for mitochondrial input variants ([pr245](https://github.com/sigven/pcgr/pull/245))
-    - [CHANGELOG](https://sigven.github.io/cpsr/articles/CHANGELOG.html)
-
+    -   patch with bug fix for mitochondrial input variants ([pr245](https://github.com/sigven/pcgr/pull/245))
+    -   [CHANGELOG](https://sigven.github.io/cpsr/articles/CHANGELOG.html)
 -   *June 2024*: **2.0.0 release**
-    - New HTML report generation and layout with [quarto](https://quarto.org/)
-    - Excel output supported
-    - Data bundle update
-    - Singularity/Apptainer support
-    - [CHANGELOG](https://sigven.github.io/cpsr/articles/CHANGELOG.html)
-
+    -   New HTML report generation and layout with [quarto](https://quarto.org/)
+    -   Excel output supported
+    -   Data bundle update
+    -   Singularity/Apptainer support
+    -   [CHANGELOG](https://sigven.github.io/cpsr/articles/CHANGELOG.html)
 -   *November 2022*: **1.0.1 release**
     -   Added CPSR logo (designed by [Hal Nakken](https://halvetica.net))
-
 -   *February 2022*: **1.0.0 release**
-    -   Complete restructure of code and Conda installation routines, contributed largely by the great [@pdiakumis](https://github.com/pdiakumis)
+    -   Complete restructure of code and Conda installation routines, contributed largely by the great [\@pdiakumis](https://github.com/pdiakumis)
     -   Updated data bundle
-        - ClinVar - Feb 2022
-        - CancerMine - Dec 2021
-        - UniprotKB - Nov 2021
-        - CIViC - Feb 2022
-        - GWAS catalog - Dec 2021
+        -   ClinVar - Feb 2022
+        -   CancerMine - Dec 2021
+        -   UniprotKB - Nov 2021
+        -   CIViC - Feb 2022
+        -   GWAS catalog - Dec 2021
     -   Software upgrade (VEP 105, R/BioConductor)
-    -   New documentation site ([https://sigven.github.io/cpsr](https://sigven.github.io/cpsr))
-
+    -   New documentation site (<https://sigven.github.io/cpsr>)
 
 ## Example report
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11401491.svg)](https://doi.org/10.5281/zenodo.11401491)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12734384.svg)](https://doi.org/10.5281/zenodo.12734384)
 
 ## Getting started
 
 -   [Installation instructions](https://sigven.github.io/cpsr/articles/installation.html)
 -   [Run through an example](https://sigven.github.io/cpsr/articles/running.html#example-run)
 -   Learn more about
-    * Details regarding the [CPSR input file](https://sigven.github.io/cpsr/articles/input.html), and how it should be formatted
-    * The types and contents of [CPSR output files](https://sigven.github.io/cpsr/articles/output.html)
-    * [ACMG variant classification procedure](https://sigven.github.io/cpsr/articles/variant_classification.html) used in CPSR
-    * The list of [virtual gene panels](https://sigven.github.io/cpsr/articles/virtual_panels.html) available in CPSR
+    -   Details regarding the [CPSR input file](https://sigven.github.io/cpsr/articles/input.html), and how it should be formatted
+    -   The types and contents of [CPSR output files](https://sigven.github.io/cpsr/articles/output.html)
+    -   [ACMG variant classification procedure](https://sigven.github.io/cpsr/articles/variant_classification.html) used in CPSR
+    -   The list of [virtual gene panels](https://sigven.github.io/cpsr/articles/virtual_panels.html) available in CPSR
 
 ## Citation
 

diff --git a/pkgdown/index.md b/pkgdown/index.md
@@ -4,19 +4,20 @@
 
 <br><br>
 
-The *Cancer Predisposition Sequencing Reporter (CPSR)* is a computational workflow that **interprets germline variants** identified from next-generation sequencing **in the context of cancer predisposition**. 
+The *Cancer Predisposition Sequencing Reporter (CPSR)* is a computational workflow that **interprets DNA sequence variants** identified from next-generation sequencing **in the context of cancer predisposition**. 
 
-*CPSR* accepts a query file with raw germline variant calls (SNVs/InDels) from a single sample (cancer patient), encoded in the [VCF format ](https://samtools.github.io/hts-specs/VCFv4.2.pdf). CPSR conducts comprehensive gene and variant annotation on the input calls, and generates a dedicated _variant HTML report_, that provides the following main functionality:
+*CPSR* accepts a query file with _germline_ variant calls (SNVs/InDels) from a single sample (i.e. cancer patient), encoded in the [VCF format ](https://samtools.github.io/hts-specs/VCFv4.2.pdf). Through comprehensive gene and variant annotation procedures, CPSR offers the following main functionalities to the user:
 
-1) Flexible **selection of cancer predisposition genes** subject to analysis and reporting
-2) **Variant classification** (*Pathogenic* to _Benign_) through implementation of ACMG guidelines
-3) **Biomarker matching** of sample variants (prognosis, diagnosis, drug sensitivity/resistance)
-4) Reporting of **secondary/incidental findings** (ACMG recommendations)
+1) Flexible **selection of cancer predisposition genes** subject to analysis and reporting - through the use of virtual gene panels
+2) **Variant classification** (*Pathogenic* to _Benign_) through a dedicated implementation of [ACMG/AMP guidelines](https://pubmed.ncbi.nlm.nih.gov/25741868/)
+3) **Detection of germline biomarkers** - for prognosis, diagnosis, or drug sensitivity/resistance
+4) Reporting of **secondary/incidental findings** ([ACMG recommendations](https://pubmed.ncbi.nlm.nih.gov/37347242/))
+5) **Interactive HTML output report** with detailed variant information, gene annotations, and external links to relevant databases
 
 
-The workflow is integrated with the framework that underlies [Personal Cancer Genome Reporter - PCGR ](https://github.com/sigven/pcgr). While *PCGR* is intended for reporting and analysis of somatic variants detected in a tumor, *CPSR* is intended for reporting and ranking of germline variants in protein-coding genes that are implicated in cancer predisposition and inherited cancer syndromes.
+The CPSR workflow is integrated with the framework that underlies [Personal Cancer Genome Reporter - PCGR ](https://github.com/sigven/pcgr). While *PCGR* is intended for reporting and analysis of somatic variants detected in a tumor, *CPSR* is intended for reporting and ranking of germline variants in protein-coding genes that are implicated in cancer predisposition and inherited cancer syndromes.
 
-Snapshots of sections in the [quarto](https://quarto.org)-based cancer predisposition genome report ((artificial sample, with more findings than usual):
+Snapshots of sections in the [quarto](https://quarto.org)-based cancer predisposition genome report (artificial sample, with more findings than usual):
 
 ![](img/cpsr_sc.png)
 
@@ -44,18 +45,10 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos
   * Software upgrade (VEP, R/BioConductor)
   * New documentation site (https://sigven.github.io/cpsr)
 
-* *June 30th 2021*: **0.6.2 release**
-  * Updated bundle (ClinVar, CancerMine, UniprotKB, PanelApp, CIViC, GWAS catalog)
-  * Software upgrade (VEP, R/BioConductor)
-  * [CHANGELOG](http://cpsr.readthedocs.io/en/latest/CHANGELOG.html)
-* *November 30th 2020*: **0.6.1 release**
-  * Updated bundle (ClinVar, CancerMine, UniprotKB, CIViC, GWAS catalog)
-  * [CHANGELOG](http://cpsr.readthedocs.io/en/latest/CHANGELOG.html)
-
 
 ### Example report
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11401491.svg)](https://doi.org/10.5281/zenodo.11401491)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12734384.svg)](https://doi.org/10.5281/zenodo.12734384)
 
 ### Getting started