Judy-generator tool experiment for master-thesis
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Updated
Nov 10, 2017 - Python
Judy-generator tool experiment for master-thesis
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.
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…
Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples
MEMDS (Mutation Enrichment followed by upscaled Maximum Depth Sequencing) protocol output analysis pipeline
Reports frequency of all single nucleotide changes for a group of fastq files
Mutation Detection in Lung Cancer Cell Lines using CNNs
Term project for the Computational Biology (ENS210) course in Sabancı University.
Generate a rich feature space describing all possible mutations in a given protein sequence (+ structure)
Python script for detecting mutations in aligned reads (.bam |.sam) e.g. from RNA base conversion techniques such as TimeLapse, SLAM-seq, TUC-seq
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.
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.
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.
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.
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…
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