The project can be accessed live here or you can run a web server on your local machine using something like MAMP.
Our final report is the file KingMorganShapiro_report.pdf and our presentation shown in class is KingMorganShapiro_presentation.pdf.
In order to generate our data we used the Genome in a Bottle Consortium's AJtrio_HiSeq300X_cortex_variants_GRCh37_09042015.vcf which can be downloaded from their FTP server: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis
For the disease names we used DisGeNET's all_variant_disease_associations.tsv which can be downloaded from https://www.disgenet.org/downloads.
The css files used for the project. It is mostly bootstrap.
There are two files here, data.tsv and data_removed_NA_genes.tsv.
We realized after performing our pre-processing steps that not all variants had known genes.
We simply removed these variants from our dataset and used data_removed_NA_genes.tsv moving forward.
Custom images used for the project. We only used one, royalty-free, permissively licensed icon which we recolored.
The Javascript files used for the project. We implemented these ourselves and used some example code from the d3 documentation, cited in comments.
The preprocessing steps we used to work with the data provided by the Genome in a Bottle Consortium.
These are the Overview page, Disease Explorer page, and Chromosome modals respectively.