Classifying mutagenic origins

MACHINE LEARNING METHODOLOGIES IN THE DISCOVERY OF THE INTERACTION BETWEEN GENES IN COMPLEX DISEASES

Ricardo José
Moreira Pinho
Dissertação De
Mestrado Apresentada
À Faculdade
De Engenharia
Da Universidade
Do Porto Em
Faculdade De
Engenharia Da
Universidade Do Porto
Ricardo Pinho
Supervisor Rui Camacho
Ricardo Pinho
Mestrado Integrado
Engenharia Informática Computação

January 2014

Machine Learning methodologies in the discovery of the interaction between genes in complex disease

COVID-19 Pandemic Stages Identification Using Machine Learning

S. Rayhan Kabir
Shomoita Jahid Mitin
Muhammad Jafar Sadeq
Umme Habiba
Roy D Gregori Ayon
Md. Sanaullah Rabbi

November 2022

Here, we used python programming language as the Machine Learning process for identifying COVID-19 s...

data for CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9

Pedersen, L

This is the raw NGS sequencing data as python analysis for the paper thats currently titled: CasPER,...

Classifying mutagenic origins

Yicheng Zhu
Ong, Cheng Soon
Huttley, Gavin

June 2018

Source code demonstrating machine learning techniques for classifying mutagenic origins. Written in ...

Supplementary for "Machine learning techniques for classifying the mutagenic origins of point mutations"

Zhu, Yicheng
Ong, Cheng Soon
Huttley, Gavin

March 2020

Supplementary tables and figures for the article “Machine learning techniques for classifying the mu...

Source code for "Genome-wide analysis of somatic noncoding mutation patterns in cancer"

Felix Dietlein
Alex B. Wang
Christian Fagre
Anran Tang
Nicolle Besselink
Edwin Cuppen
Chunliang Li
Shamil R. Sunyaev
James T. Neal
Eliezer M. Van Allen

January 2022

Source code and user manual to execute it for the manuscript "Genome-wide analysis of somatic noncod...

Synthetic supervised learning for cancer evolution inference

Tom W Ouellette

January 2022

Code, figures, and data for analyses outlined in "Inferring cancer evolution from single tumour biop...

Python code for statistical analysis of MScore data to identify DNA methylation signatures for early detection of hepatocellular carcinoma (HCC)

Cheishvili David

April 2023

This Python code performs statistical analysis on MScore data related to DNA methylation to identify...

Analysis source code for: Peneder et al. "Multimodal analysis of cell-free DNA whole genome sequencing for pediatric cancers with low mutational burden", Nature Communications (2021)

Peneder Peter

April 2021

This .zip file contains the source code necessary to replicate the key aspects of the analysis prese...

Code accompanying "Analysis of Targeted and Combinatorial Approaches to Phage T7 Genome Generation" Master's Thesis

Mallet, Alex
Endy, Drew

November 2006

This submission is a zip file containing the code used to generate the results described in Alex Mal...

3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints

Won, Dhong-gun
Kim, Dong-wook
Woo, Junwoo Isaac
Lee, Kyoungyeul

July 2021

Dataset needed to train and evaluate 3Cnet. See github repository for source code. https://github....

Matlab Code for "Predicting Exposure to Ionizing Radiation by Biochemically-Inspired Genomic Machine Learning"

Zhao, Jonathan Z.L.
Mucaki, Eliseos J.
Rogan, Peter K.

February 2018

This file contains the Matlab code associated with the publication "Predicting Exposure to Ionizing ...

Code for "Computational analysis of pathological image enables interpretable prediction for microsatellite instability"

Zhu, J

The Python and R source code for reproducing the result in "Computational analysis of pathological i...

Additional file 6 of Development of machine learning classifiers to predict compound activity on prostate cancer cell lines

Davide Bonanni (5491928)
Luca Pinzi (6268934)
Giulio Rastelli (1513714)

November 2022

Additional file 6. Python script to generate the initial PC-3, DU-145 and PC-3/DU-145 dataset

MutaCheck: A novel pipeline to check for single nucleotide polymorphism (SNP) and associated diseases in mitochondrial DNA

Harini Subramaniam
P Dhruthi
Devashish Devashish
V Suchithra
Vidya Niranjan

January 2021

This project utilizes various online tools and databases along with uniquely written codes to give a...

MACHINE LEARNING METHODOLOGIES IN THE DISCOVERY OF THE INTERACTION BETWEEN GENES IN COMPLEX DISEASES

Ricardo José
Moreira Pinho
Dissertação De
Mestrado Apresentada
À Faculdade
De Engenharia
Da Universidade
Do Porto Em
Faculdade De
Engenharia Da
Universidade Do Porto
Ricardo Pinho
Supervisor Rui Camacho
Ricardo Pinho
Mestrado Integrado
Engenharia Informática Computação

January 2014

Machine Learning methodologies in the discovery of the interaction between genes in complex disease

COVID-19 Pandemic Stages Identification Using Machine Learning

S. Rayhan Kabir
Shomoita Jahid Mitin
Muhammad Jafar Sadeq
Umme Habiba
Roy D Gregori Ayon
Md. Sanaullah Rabbi

November 2022

Here, we used python programming language as the Machine Learning process for identifying COVID-19 s...

data for CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9

Pedersen, L

This is the raw NGS sequencing data as python analysis for the paper thats currently titled: CasPER,...

Classifying mutagenic origins

Yicheng Zhu
Ong, Cheng Soon
Huttley, Gavin

June 2018

Source code demonstrating machine learning techniques for classifying mutagenic origins. Written in ...

Supplementary for "Machine learning techniques for classifying the mutagenic origins of point mutations"

Zhu, Yicheng
Ong, Cheng Soon
Huttley, Gavin

March 2020

Supplementary tables and figures for the article “Machine learning techniques for classifying the mu...

Source code for "Genome-wide analysis of somatic noncoding mutation patterns in cancer"

Felix Dietlein
Alex B. Wang
Christian Fagre
Anran Tang
Nicolle Besselink
Edwin Cuppen
Chunliang Li
Shamil R. Sunyaev
James T. Neal
Eliezer M. Van Allen

January 2022

Source code and user manual to execute it for the manuscript "Genome-wide analysis of somatic noncod...

Synthetic supervised learning for cancer evolution inference

Tom W Ouellette

January 2022

Code, figures, and data for analyses outlined in "Inferring cancer evolution from single tumour biop...

Python code for statistical analysis of MScore data to identify DNA methylation signatures for early detection of hepatocellular carcinoma (HCC)

Cheishvili David

April 2023

This Python code performs statistical analysis on MScore data related to DNA methylation to identify...

Analysis source code for: Peneder et al. "Multimodal analysis of cell-free DNA whole genome sequencing for pediatric cancers with low mutational burden", Nature Communications (2021)

Peneder Peter

April 2021

This .zip file contains the source code necessary to replicate the key aspects of the analysis prese...

Code accompanying "Analysis of Targeted and Combinatorial Approaches to Phage T7 Genome Generation" Master's Thesis

Mallet, Alex
Endy, Drew

November 2006

This submission is a zip file containing the code used to generate the results described in Alex Mal...

3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints

Won, Dhong-gun
Kim, Dong-wook
Woo, Junwoo Isaac
Lee, Kyoungyeul

July 2021

Dataset needed to train and evaluate 3Cnet. See github repository for source code. https://github....

Matlab Code for "Predicting Exposure to Ionizing Radiation by Biochemically-Inspired Genomic Machine Learning"

Zhao, Jonathan Z.L.
Mucaki, Eliseos J.
Rogan, Peter K.

February 2018

This file contains the Matlab code associated with the publication "Predicting Exposure to Ionizing ...

Code for "Computational analysis of pathological image enables interpretable prediction for microsatellite instability"

Zhu, J

The Python and R source code for reproducing the result in "Computational analysis of pathological i...

Additional file 6 of Development of machine learning classifiers to predict compound activity on prostate cancer cell lines

Davide Bonanni (5491928)
Luca Pinzi (6268934)
Giulio Rastelli (1513714)

November 2022

Additional file 6. Python script to generate the initial PC-3, DU-145 and PC-3/DU-145 dataset

MutaCheck: A novel pipeline to check for single nucleotide polymorphism (SNP) and associated diseases in mitochondrial DNA

Harini Subramaniam
P Dhruthi
Devashish Devashish
V Suchithra
Vidya Niranjan

January 2021

This project utilizes various online tools and databases along with uniquely written codes to give a...

MACHINE LEARNING METHODOLOGIES IN THE DISCOVERY OF THE INTERACTION BETWEEN GENES IN COMPLEX DISEASES

Ricardo José
Moreira Pinho
Dissertação De
Mestrado Apresentada
À Faculdade
De Engenharia
Da Universidade
Do Porto Em
Faculdade De
Engenharia Da
Universidade Do Porto
Ricardo Pinho
Supervisor Rui Camacho
Ricardo Pinho
Mestrado Integrado
Engenharia Informática Computação

January 2014

Machine Learning methodologies in the discovery of the interaction between genes in complex disease

COVID-19 Pandemic Stages Identification Using Machine Learning

S. Rayhan Kabir
Shomoita Jahid Mitin
Muhammad Jafar Sadeq
Umme Habiba
Roy D Gregori Ayon
Md. Sanaullah Rabbi

November 2022

Here, we used python programming language as the Machine Learning process for identifying COVID-19 s...

data for CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9

Pedersen, L

This is the raw NGS sequencing data as python analysis for the paper thats currently titled: CasPER,...

Classifying mutagenic origins

Abstract

Extracted data

Classifying mutagenic origins

Abstract

Extracted data

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