This tools visualizes homology of given protein change e.g. NP_001501.2:p.Arg121Leu using texshade. Texshade is a latex package for setting nucleotide and peptide alignments. Multiple sequence alignments for the proteins are retrieved from NCBI homologene database. The tool is useful for visualizing a variant on evulotionary conserved regions. The source code is available on GitHub.
This tool maps aliases, and previous or withdrawn symbols to current approved HGNC symbols as well as check for any entries that are not gene symbols and fix capitalizations. Ensembl and RefSeq annotation files sometimes use previous or alias symbols. This tool also cross checks against Ensembl and NCBI annotation files for different genome versions and shows which gene symbols used. This way an accurate gene set can be utilized to avoid false negatives in the variant discovery process. The source code is available on GitHub.
This tool simulates genotypes for control and case groups and performs logistic regression on score. The tools is served at shinyapps. You can read more about how it works and the the components within at this post The source code is available on GitHub.