Institute for Medical Genetics and Applied Genomics (IMGAG)
A tool to identify transmembrane proteins from a given list of gene or protein IDs. Read More.
A tool to convert given gene IDs to various other IDs. (under development, please come back later). Read More.
Gene4mVCF is a Python package that allows you to extract variant entries for specific genes or a list of genes from a VCF (Variant Call Format) file. It utilizes tools like bcftools, tabix, and Python libraries like pysam, pandas, pybedtools, tqdm, and gffutils to efficiently parse and extract variants. Read More.
The tool gwas2vcf can convert GWAS results files, like the .tsv.bgz files from UK Biobank studies, into the standard VCF 4.0 format. For best results, it's recommended to create a virtual environment with Python 3.11.6, as that's the version this tool was tested with. Read More.
A tool to detect STAT3-enhancing germline receptor variant (STAT3-eGRV). (Under Production)..
TraPS VarI is a tool to identify membrane-proximal tyrosine-based sequence motifs YxxQ, where Y is tyrosine, Q is glutamine and x any amino acid. It is a python based module for predicting germline receptor variants of single-pass transmembrane proteins potentially capable of modulating in a genotype-dependent manner, the STAT3 signaling and drug sensititiviy to growth inhibition (Ulaganathan et al, 2015; doi:10.1038/nature16449). The algorithm requires single nucleotide polymorphism genotyping datasets in Variable Call Format 4.0 as input. Additionally, the tool finds for associated membrane proteins, all the matching therapeutic target database and DrugBank records. Read More.