An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: mutation-analysis

infection/infection

PHP Mutation Testing library

Language: PHP - Size: 48.2 MB - Last synced at: 23 minutes ago - Pushed at: about 8 hours ago - Stars: 2,100 - Forks: 164

datagone/vscode-stryker-mutator

Unofficial VSCode extension of 'Stryker Mutator' for hunting mutants hiding in our codebase (currently, it supports .NET)

Language: TypeScript - Size: 3.05 MB - Last synced at: about 15 hours ago - Pushed at: about 16 hours ago - Stars: 3 - Forks: 0

theofidry/awesome-mutation-testing

Mutation testing resources: how to make better code by introducing bugs

Size: 105 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 424 - Forks: 38

sebastian-gregoricchio/SPACCa

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

Language: Python - Size: 4.74 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 0

hcoles/pitest

State of the art mutation testing system for the JVM

Language: Java - Size: 14.2 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 1,743 - Forks: 354

zalanlevai/mutest-rs

Mutation testing tools for Rust

Language: Rust - Size: 2.71 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 13 - Forks: 1

sualeh/introduction-to-mutation-testing

Introduction to Mutation Testing

Language: C# - Size: 828 KB - Last synced at: 13 days ago - Pushed at: 14 days ago - Stars: 23 - Forks: 5

mull-project/mull

Practical mutation testing and fault injection for C and C++

Language: C++ - Size: 6.07 MB - Last synced at: 15 days ago - Pushed at: 22 days ago - Stars: 769 - Forks: 76

AlexandrovLab/SigProfilerMatrixGenerator

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.

Language: Python - Size: 1 GB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 107 - Forks: 40

nodrogluap/tamor

Illumina Dragen cancer genome and transcriptome analysis automation using Snakemake

Language: Python - Size: 381 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 7 - Forks: 1

haliliceylan/MUT4SLX

The Simulink Model Mutation Testing project provides a framework for generating mutants, and CSV file as an output. It utilizes the MATLAB environment to load the model, apply mutations, and collect outputs.

Language: HTML - Size: 17.9 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 1

AlexandrovLab/SigProfilerPlotting

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.

Language: Python - Size: 89.7 MB - Last synced at: 8 days ago - Pushed at: 3 months ago - Stars: 48 - Forks: 15

ValldHebron-Bioinformatics/minMutFinder

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.

Language: Python - Size: 79.7 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 1 - Forks: 0

infection/playground

Infection Playground - online tool to try Infection right in your browser.

Language: PHP - Size: 18.1 MB - Last synced at: 2 days ago - Pushed at: 28 days ago - Stars: 3 - Forks: 2

AlexandrovLab/SigProfilerExtractor

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 SigProfilerMatrixGenerator and SigProfilerPlotting.

Language: Python - Size: 166 MB - Last synced at: 27 days ago - Pushed at: 29 days ago - Stars: 158 - Forks: 54

humbug/humbug 📦

Humbug is a Mutation Testing framework for PHP to measure the real effectiveness of your test suites and assist in their improvement. It eats Code Coverage for breakfast.

Language: PHP - Size: 968 KB - Last synced at: 6 days ago - Pushed at: over 7 years ago - Stars: 1,129 - Forks: 70

ChmielewskiKamil/checkmate

Testing the mutations generated by Gambit.

Language: Go - Size: 24.4 KB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 1 - Forks: 0

Optimized-Brain/MutAIon

A Full Stack Variant Effect Predictor leveraging the Evo2 LLM for Single Nucleotide Variant(SNV) pathogenicity analysis, powered by a Modal‑deployed FastAPI GPU backend and a Next.js + Shadcn UI frontend

Language: TypeScript - Size: 15.2 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

jajik123/GenAnalyzer

GenAnalyzer is a web application designed for the analysis of protein sequences, mutation detection, and exploring their links to genetic diseases. Built using Flask, this tool integrates data from UniProt and ClinVar for efficient bioinformatics analysis.

Language: JavaScript - Size: 2.03 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

livnat-lab/HBB_HBD

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

Language: Python - Size: 179 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

AlexandrovLab/SigProfilerExtractorR

An R wrapper for SigProfilerExtractor that 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 SigProfilerMatrixGenerator and SigProfilerPlotting.

Language: R - Size: 676 KB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 15 - Forks: 1

EngineeringSoftware/mcoq

Mutation analysis tool for Coq verification projects

Language: Java - Size: 1.9 MB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 29 - Forks: 1

AlexandrovLab/SigProfilerClusters

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.

Language: Python - Size: 1.7 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 12 - Forks: 1

mohrez86/pyllmut

A research-based LLM-driven mutant generator library for Python

Language: Python - Size: 91.8 KB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

AlexandrovLab/SigProfilerTopography

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.

Language: Python - Size: 5.06 MB - Last synced at: 27 days ago - Pushed at: 4 months ago - Stars: 19 - Forks: 1

madsondeluna/getvar_containerized

O GetVar é útil para o auxílio a diagnósticos genéticos e aconselhamentos, permitindo decisões baseadas em dados com respaldo científico, otimizando tempo e servindo de suporte ao sistema de decisão clínico.

Language: HTML - Size: 330 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

AlexandrovLab/SigProfilerPlottingR

An R wrapper for running the SigProfilerPlotting framework

Language: R - Size: 861 KB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 10 - Forks: 1

infection/homebrew-infection

Homebrew tap for https://infection.github.io/

Language: Ruby - Size: 13.7 KB - Last synced at: about 7 hours ago - Pushed at: 6 months ago - Stars: 5 - Forks: 1

eringill/chronic_infection_python

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.

Language: Python - Size: 11.1 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 2 - Forks: 1

STAMP-project/pitest-descartes

Descartes supports developers to improve their test suites by reporting weak spots in covered code

Language: Java - Size: 2.82 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 126 - Forks: 21

lisabensoussan/DNA_lab

This project provides hands-on experience in DNA analysis using R, covering sequence manipulation, mutation analysis, GC content, fragment analysis, sequence alignment, RNA-seq, variant analysis, and phylogenetics.

Language: HTML - Size: 6.51 MB - Last synced at: 4 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

akshaydake123/Mutation-Testing

Projects that use mutation testing, based on mutation operators applied at the level of a statement within a method or a function. The mutated program needs to be strongly killed by the designed test cases. At least three different mutation operators should be used.

Language: Java - Size: 3.77 MB - Last synced at: 10 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

ojcharles/MutationFeatures

Generate a rich feature space describing all possible mutations in a given protein sequence (+ structure)

Language: Python - Size: 1.06 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 5 - Forks: 1

phantran/moco

An efficient mutation testing tool written in Kotlin for Java Maven projects

Language: Kotlin - Size: 643 KB - Last synced at: 6 months ago - Pushed at: about 4 years ago - Stars: 3 - Forks: 1

studyfair/studyfair

Student plagiarism detection tool based on CCD algorithms

Language: Ruby - Size: 566 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

IbrahimTanyalcin/I-PV

Interactive Protein Sequence VIsualization/Viewer - Interactive Circos

Language: HTML - Size: 66.6 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 10 - Forks: 1

scoban/mutation-analysis

Experimental Evaluation and Comparison of Java Mutation Tools

Language: Shell - Size: 29.8 MB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 1

STAMP-project/pitmp-maven-plugin

Maven plugin to handle multi module projects for PiTest

Language: Java - Size: 2.69 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 44 - Forks: 14

magsilva/proteum

Tool for mutation testing of C programs

Language: C - Size: 2.25 MB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 19 - Forks: 10

seer-lab/MutationScorePredictor

A project that will predict the mutation score of methods and classes using a support vector machine and source code metrics

Language: Ruby - Size: 392 KB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 0

INDEINS/DENV-OUTBREAK

Genomic surveillance for Dengue peruvian outbreaks

Language: Shell - Size: 543 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

AjNavneet/GeneticMutation_Classifier

Multi-class classifier for DNA genetic mutations.

Language: Jupyter Notebook - Size: 3.25 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

paulashford/funvar-tracerx

Collated scripts for FunVar-TRACERx gene duplication, diversity and neofun.

Language: R - Size: 5.92 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

gorkemkose/ENS210_Computational_Biology_Project

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

Language: Python - Size: 10.2 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

Mashin6/detect-mutations

Python script for detecting mutations in aligned reads (.bam |.sam) e.g. from RNA base conversion techniques such as TimeLapse, SLAM-seq, TUC-seq

Language: Python - Size: 5.86 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 2

thierry-tct/mart

LLVM Mutation Artisan (MART) is a configurable mutation testing framework based on LLVM

Language: C++ - Size: 80.8 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 25 - Forks: 6

tiagoantonio/woland

WOLAND is a multiplatform tool to analyze point mutation patterns using resequencing data from any organism or cell. It is implemented as a Perl and R tool using as inputs filtered unannotated or annotated SNV lists, combined with its correspondent genome sequences.

Language: Perl - Size: 2.62 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 3

AlexandrovLab/SigProfilerMatrixGeneratorR

R wrapper for utilizing the SigProfilerMatrixGenerator framework

Language: R - Size: 1.42 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 20 - Forks: 4

GZoltar/killmap

Utility Java program to perform mutation-analysis

Language: Java - Size: 43.9 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 3 - Forks: 1

hrbigelow/depngs

Next-gen Sequencing analysis tools

Language: C - Size: 2.05 MB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ninadakolekar/KRAS-Mutation-Detection 📦

Mutation Detection in Lung Cancer Cell Lines using CNNs

Language: Python - Size: 58.6 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

ali-ghanbari/memu-demo

Faster Mutation Analysis with MeMu

Language: Java - Size: 7.03 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0

Noam-Hadar/BAMdelbee

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 ones in question. We hereby demonstrate how our application can spot homozygous deletions absent from VCF files for being too vast, yet undetectable by chromosomal microarrays (CMA) for being too small. The application is freely available on our website and can run on a common laptop. Therefore, we recommend integrating it into WES and WGS interpretation pipelines for recessive diseases.

Language: Python - Size: 39.8 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

uds-helms/MutaNET

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

Language: Python - Size: 333 MB - Last synced at: 7 months ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 1

reimandlab/needleplot

Another needleplot for mutation data, used by ActiveDriverDB

Language: JavaScript - Size: 52.7 KB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

christoffer-nylen/dexcov

Generates a Dextool Mutate vs LCOV side by side presentation

Language: HTML - Size: 762 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

drake69/epimut

Stochastic Epimutation Finder

Language: R - Size: 35.2 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

sung/nectarmutation.org

things behind nectarmutation.org

Language: Perl - Size: 2.45 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

rcs333/frequency-scanner

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

Language: Python - Size: 27.3 KB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

paweltatarczuk/judy-generator-experiment

Judy-generator tool experiment for master-thesis

Language: Python - Size: 30.6 MB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 2