SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.
SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of different mutational processes. SigProfilerTopography elucidates the unique topographical characteristics of mutational signatures.
Tool for analyzing the inter-mutational distances between SNV-SNV and INDEL-INDEL mutations. Tool separates mutations into clustered and non-clustered groups on a sample-dependent basis.
Generate a rich feature space describing all possible mutations in a given protein sequence (+ structure)
Illumina Dragen cancer genome and transcriptome analysis automation using Snakemake
Python script for detecting mutations in aligned reads (.bam |.sam) e.g. from RNA base conversion techniques such as TimeLapse, SLAM-seq, TUC-seq
A simple GUI that allows users to check whether mutations from a SARS-CoV-2 genome best fit a mutational distribution of genomes derived from global, chronic, or deer infections.
A research-based LLM-driven mutant generator library for Python
Term project for the Computational Biology (ENS210) course in Sabancı University.
Tool written in Python and Bash implemented in a Nextflow pipeline that accurately identifies mutations and assesses their frequencies, accounting for multiple nucleotide mutations occurring within a single codon. Additionally, it can annotate mutations associated to phenotypical changes in viral populations based on user-supplied datasets.
A deep learning framework for HIV-1 drug resistance prediction using context-aware fusion of sequence and mutation features, with hybrid rule–model evaluation and robustness analysis. The model demonstrates adaptive feature reliance and strong cross-drug generalization.
Python tool for analyzing protein point mutations. Calculates changes in molecular weight, charge, and hydrophobicity. Classifies mutations by severity and generates visualizations and HTML reports.
Automated analysis tool for mutations in promoters, transcription factor binding sites, coding regions and protein domains in the context of gene regulatory networks.
Mutation Detection in Lung Cancer Cell Lines using CNNs
Judy-generator tool experiment for master-thesis
Set of programs for assessing the mutations from a set of amino acid sequences.
DNA mutation analysis and protein impact interpretation
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