MuRaL is a deep learning framework for estimating single-nucleotide mutation rates across the genome.
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Jul 1, 2024 - Python
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mutation-rate
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Nextflow pipeline for estimation of evolutionary rate using Bayesian statistics.
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Aug 12, 2022 - Nextflow
Reports frequency of all single nucleotide changes for a group of fastq files
next-generation-sequencing metagenomics transitions mutation-analysis fastq-anaysis mutation-rate transversions
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Jan 13, 2020 - Python
Algorithms for the generation of substitution matrices from intra-taxa variation data. Implemented and published on human genetic variation data.
bioinformatics genomics biology bioinformatics-pipeline proteomics phosphorylation amino-acids bioinformatics-algorithms substitution-models mutational-signatures bioinformatics-tool post-translational-modification mutation-rate
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Jun 18, 2021 - Jupyter Notebook
A biologically motivated mathematical formalism is used to estimate the relative risks of breast, lung and thyroid cancers in childhood cancer survivors due to concurrent therapy regimen. This model specifically includes possible organ-specific interaction between radiotherapy and chemotherapy. The model predicts relative risks for developing se…
treatment-effects radiotherapy chemotherapy mutation-rate relative-risk second-cancer childhood-cancer-survivors-study chemo-radiation treatment-interaction concurrent-therapy
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Oct 14, 2018 - MATLAB
We employed a biologically motivated mathematical model to estimate the radiation and chemotherapy-induced relative risks of thyroid malignancies in four childhood cancer study survivors (CCSS) data sets. the predictions of radiation and chemotherapy-induced relative risks of secondary thyroid malignancies using the mathematical model are compar…
radiation chemotherapy mutation-rate radiation-therapy relative-risk second-cancer thyroid-malignancies
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Oct 14, 2018 - MATLAB
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