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.

Mutation Detection in Lung Cancer Cell Lines using CNNs

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.

Term project for the Computational Biology (ENS210) course in Sabancı University.

Judy-generator tool experiment for master-thesis

Mutation Analysis of perceptions of people towards GMOs

Set of programs for assessing the mutations from a set of amino acid sequences.

MEMDS (Mutation Enrichment followed by upscaled Maximum Depth Sequencing) protocol output analysis pipeline

Automated analysis tool for mutations in promoters, transcription factor binding sites, coding regions and protein domains in the context of gene regulatory networks.

BAMdelbee is a novel tool for discovering homozygous deletions in Whole-exome-sequencing (WES) and whole-genome-sequencing (WGS) data. WES or WGS samples generated by the same method produce BAM files with similar alignment coverage across the genome. BAMdelbee locates homozygous deletions by pinpointing regions covered in all samples but the on…

Reports frequency of all single nucleotide changes for a group of fastq files

Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples