WIP Update course for pVACtools 6.0

Author: susannasiebert

docs/01-intro.md

@@ -3,7 +3,7 @@
 
 # Introduction
 
-This course has been developed recently (Summer 2023). We welcome any feedback at help@pvactools.org or by submission of [GitHub issues](https://github.com/griffithlab/pVACtools_Intro_Course/issues).
+This course was developed in Summer 2023 and updated in Fall 2025. We welcome any feedback at help@pvactools.org or by submission of [GitHub issues](https://github.com/griffithlab/pVACtools_Intro_Course/issues).
 
 ## Motivation
 
@@ -17,11 +17,11 @@ allele expression, peptide binding affinities, and determination of whether a mu
 users to efficiently generate, review, and interpret results, selecting candidate peptides for individual experiments or patient vaccine designs. Additional modules
 support design choices needed for competing vaccine delivery approaches. One such module optimizes peptide ordering to minimize junctional epitopes in DNA vector
 vaccines. Downstream analysis commands for synthetic long peptide vaccines are available to assess candidates for factors that influence peptide synthesis. All
-of the aforementioned steps are executed via a modular workflow consisting of tools for neoantigen prediction from somatic alterations (pVACseq, pVACfuse, and pVACbind),
+of the aforementioned steps are executed via a modular workflow consisting of tools for neoantigen prediction from somatic alterations (pVACseq, pVACfuse, pVACsplice, and pVACbind),
 prioritization, and selection using a graphical Web-based interface (pVACview), and design of DNA vector–based vaccines (pVACvector) and synthetic long peptide
 vaccines. pVACtools is available at [http://www.pvactools.org](http://www.pvactools.org).
 
-<img src="resources/images/01-intro_files/figure-html//1uz39zaObDGKhEVCGzO0JO35CTbC0oRAM0mxgLcMAA9Y_g22b1533a196_0_0.png" title="pVACtools is a cancer immunotherapy tools suite" alt="pVACtools is a cancer immunotherapy tools suite" width="100%" style="display: block; margin: auto;" />
+<img src="resources/images/01-intro_files/figure-html//1uz39zaObDGKhEVCGzO0JO35CTbC0oRAM0mxgLcMAA9Y_g3a37485c18b_1_0.png" title="pVACtools is a cancer immunotherapy tools suite" alt="pVACtools is a cancer immunotherapy tools suite" width="100%" style="display: block; margin: auto;" />
 
 ## Background
 

docs/02-prerequisites.md

@@ -62,6 +62,9 @@ install.packages("RCurl", dependencies=TRUE)
 install.packages("curl", dependencies=TRUE)
 install.packages("string", dependencies=TRUE)
 install.packages("shinycssloaders", dependencies=TRUE)
+install.packages("plotly", dependencies=TRUE)
+install.packages("shinyWidgets", dependencies=TRUE)
+install.packages("colourpicker", dependencies=TRUE)
 ```
 
 ## Data
@@ -96,20 +99,40 @@ For pVACfuse:
 - `star-fusion.fusion_predictions.tsv`: A STARFusion prediction file with fusion read support
   and expression information.
 
+For pVACsplice:
+
+- `HCC1395.splice_junctions.tsv`: A RegTools junctions output TSV file
+
 General:
 
 - `Homo_sapiens.GRCh38.pep.all.fa.gz`: A reference proteome peptide FASTA to use
   for determining whether there are any reference matches of neoantigen candidates.
 
 To download this data, please run the following commands:
 
-
 ```bash
 wget https://raw.githubusercontent.com/griffithlab/pVACtools_Intro_Course/main/HCC1395_inputs.zip
 unzip HCC1395_inputs.zip
 ```
 
+Additionally, to run pVACsplice, a set of reference files are required that
+are too large to include in the HCC1395_inputs.zip archive. To download these
+manually please run the following commands:
+
+```bash
+cd HCC1395_inputs
+wget https://ftp.ensembl.org/pub/release-105/gtf/homo_sapiens/Homo_sapiens.GRCh38.105.chr.gtf.gz
+wget http://genomedata.org/pmbio-workshop/references/genome/all/ref_genome.tar
+tar -xf ref_genome.tar ref_genome.fa.gz ref_genome.fa.fai
+gunzip ref_genome.fa.gz
+rm -rf ref_genome.tar
+```
+
+This will add the following reference files
+
+- `ref_genome.fa` and `.fai`: A reference DNA FASTA file and index
+- `Homo_sapiens.GRCh38.105.chr.gtf.gz`: A reference GTF file
+
 This course will not cover the required pre-processing steps for the pVACtools
 input data but extensive instructions on how to prepare your own data for use
 with pVACtools can be found at [pvactools.org](http://www.pvactools.org).
-