Python Cancer-genomics Resources

93_Python_Data_Analytics_Projects This repository contains all the data analytics projects that I've worked on in python. No. Name 01 001_Cervical_Can

Project summary This repository contains the implementation of my bachelor degree project. The aim of the project is to apply non-linear feature reduc

Contextual Attention Network: Transformer Meets U-Net Contexual attention network for medical image segmentation with state of the art results on skin

Breast-Cancer-Detection Breast cancer is the most frequent cancer among women, with around one in every 19 women at risk. The number of cases of breas

bayesian_uncertainty This is my research project for the Irving Center for Cancer Dynamics/Azizi Lab, Columbia University. In this project I build a s

SCI-AIDE : High-fidelity Few-shot Histopathology Image Synthesis for Rare Cancer Diagnosis Pretrained Models In this work, we created synthetic tissue

SubOmiEmbed: Self-supervised Representation Learning of Multi-omics Data for Cancer Type Classification

Anomaly-detection-Feature-Selection Evaluate on three different ML model for feature selection using Breast cancer data. ML models: SVM, KNN and MLP.

Breast cancer is been classified into benign tumour and malignant tumour. Logistic regression is applied in this model.

Breast Cancer Classification Model is applied on a different dataset

Breast-Cancer-Classification - Using SKLearn breast cancer dataset which contains 569 examples and 32 features classifying has been made with 6 different algorithms

Breast-Cancer-Prediction Trying to predict whether the cancer is benign or malignant using REGRESSION MODELS in Python. Team Members NAME ROLL-NUMBER

This is a Kaggle competition in which we have to identify if the given lesion image is malignant or not for Melanoma which is a type of skin cancer.

Shield: This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Deep Learning to Improve Breast

Using Convolutional Neural Networks (CNN) for Semantic Segmentation of Breast Cancer Lesions (BRCA). Master's thesis documents. Bibliography, experiments and reports.

CellRank's reproducibility repository We believe that reproducibility is key and have made it as simple as possible to reproduce our results. Please e

To Design and Implement Logistic Regression to Classify Between Benign and Malignant Cancer Types, from a Database Taken From Dr. Wolberg reports his Clinic Cases.

msprime msprime is a population genetics simulator based on tskit. Msprime can simulate random ancestral histories for a sample of individuals (consis

ezancestry Easily visualize your direct-to-consumer genetics next to 2500+ samples from the 1000 genomes project. Evaluate the performance of a custom

Orbivator_AI Breast Cancer Wisconsin (Diagnostic) GOAL To Determine which features of data (measurements) are most important for diagnosing breast can

Cancer-and-Tumor-Detection-Using-Inception-model In this repo i am gonna show you how i did cancer/tumor detection in lungs using deep neural networks

Patient-Survival - Using Python, I developed a Machine Learning model using classification techniques such as Random Forest and SVM classifiers to predict a patient's survival status that have undergone breast cancer surgery.

BreastCancerDetection - This program is designed to predict two severity of abnormalities associated with breast cancer cells: benign and malignant. Mammograms from MIAS is preprocessed and features are extracted using the pre-trained CNN.

MSHT: Multi-stage Hybrid Transformer for the ROSE Image Analysis This is the official page of the MSHT with its experimental script and records. We de

HiCBrowser : A simple web browser to visualize Hi-C and other genomic tracks Fidel Ramirez, José Villaveces, Vivek Bhardwaj Installation You can insta

Naive-Bayes Predict Breast Cancer Wisconsin (Diagnostic) using Naive Bayes Downloading Data Set Use our Breast Cancer Wisconsin Data Set Also you can

Full Spectrum Bioinformatics is a free online text designed to introduce key topics in Bioinformatics using the Python programming language. The text is written in interactive Jupyter Notebooks, which allow you to try out and modify example code and analyses.

Gosling.js Gosling.js is a declarative grammar for interactive (epi)genomics visualization on the Web. ⚠️ Please be aware that the grammar of Gosling.

gos is a declarative (epi)genomics visualization library for Python. It is built on top of the Gosling JSON specification, providing a simplified interface for authoring interactive genomic visualizations.

Predicting Axillary Lymph Node Metastasis in Early Breast Cancer Using Deep Learning on Primary Tumor Biopsy Slides Project | This repo is the officia

CSAW-M This repository contains code for CSAW-M: An Ordinal Classification Dataset for Benchmarking Mammographic Masking of Cancer. Source code for tr

ContIG: Self-supervised Multimodal Contrastive Learning for Medical Imaging with Genetics This is the code implementation of the paper "ContIG: Self-s

OmiTrans Please also have a look at our multi-omics multi-task DL freamwork 👀 : OmiEmbed The FIRST GANs-based omics-to-omics translation framework Xi

Tempo: Optimizing risk-based breast cancer screening policies with reinforcement learning Introduction This repository was used to develop Tempo, as d

eCaReNet This code is for eCaReNet: explainable Cancer Relapse Prediction Network. (Towards Explainable End-to-End Prostate Cancer Relapse Prediction

OmiTrans Please also have a look at our multi-omics multi-task DL freamwork 👀 : OmiEmbed The FIRST GANs-based omics-to-omics translation framework Xi

Naivebayes text classifcation model for cancer and noncancer documents Author: Alex King Purpose Requirements/files included How to use 1. Purpose The

pyradiomics v3.0.1 Build Status Linux macOS Windows Radiomics feature extraction in Python This is an open-source python package for the extraction of

meatballs An open source recipe book from the awesome staff of Clinical Genomics.

Install vintools To download this package from pypi: pip install vintools Install the development package To download and install the developmen

Map single-cell transcriptomes to copy number evolutionary trees. Check out the tutorial for more information. Installation $ pip install scatrex SCA

Hierarchical probabilistic 3D U-Net, with attention mechanisms (—𝘈𝘵𝘵𝘦𝘯𝘵𝘪𝘰𝘯 𝘜-𝘕𝘦𝘵, 𝘚𝘌𝘙𝘦𝘴𝘕𝘦𝘵) and a nested decoder structure with deep supervision (—𝘜𝘕𝘦𝘵++). Built in TensorFlow 2.5. Configured for voxel-level clinically significant prostate cancer detection in multi-channel 3D bpMRI scans.

OG-SPACE Introduction Optimized Gillespie algorithm for simulating Stochastic sPAtial models of Cancer Evolution (OG-SPACE) is a computational framewo

Toolchest Python Client Toolchest provides APIs for scientific and bioinformatic data analysis. It allows you to abstract away the costliness of runni

SlideGraph+: Whole Slide Image Level Graphs to Predict HER2 Status in Breast Cancer A novel graph neural network (GNN) based model (termed SlideGraph+

GDBIGtools: A command line tools for GDBIG varaints browser Introduction Born in Guangzhou Cohort Study Genome Research Database is based on thousands

Multi-level-colonoscopy-malignant-tissue-detection-with-adversarial-CAC-UNet Implementation detail for our paper "Multi-level colonoscopy malignant ti

NCRF Prerequisites Data Whole slide images Annotations Patch images Model Training Testing Tissue mask Probability map Tumor localization FROC evaluat

Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening Introduction This is an implementation of the model used for breast

DeepCDR Cancer Drug Response Prediction via a Hybrid Graph Convolutional Network This work has been accepted to ECCB2020 and was also published in the

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