cancer

There are 24 repositories under cancer topic.

BMIRDS / deepslide
Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.
histopathology-images microscopy sliding-windows medical-image-analysis resnet wsi lung cancer pathology-image
Language:Python 480
nf-core / sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
nextflow workflow pipeline bioinformatics genomics cancer next-generation-sequencing conda reproducible-research containers germline somatic variant-calling nf-core gatk4 annotation whole-genome-sequencing whole-exome-sequencing pre-processing target-panels
Language:Nextflow 361
pyGeno
tariqdaouda / pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
bioinformatics biology genomics proteomics genome genome-annotation genome-browser genome-sequencing genomes medical medicine cancer cancer-genomics cancer-genomes ensembl gtf vcf snps csv-parser bed
Language:Python 309
seandavi / awesome-cancer-variant-databases
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
awesome-list cancer cancer-variants cancer-genomics mutations clinical-trials bioinformatics
292
sigven / pcgr
Personal Cancer Genome Reporter (PCGR)
cancer-genomics cancer-variants somatic interpreter reporting-engine clinical oncology-data precision-oncology vcf tumor annotation-framework annotation-tool cancer copy-number-variation snvs therapeutic-targets precision-cancer-medicine variant-interpretation
Language:R 250
suhrig / arriba
Fast and accurate gene fusion detection from RNA-Seq data
gene-fusions rna-seq cancer gene-fusion fusion-gene fusion-genes variant-calling structural-variation star virus-integration
Language:C++ 220
shobhitsrivastava-ds / ML-MT-WebApp
This project is all about a Machine Learning based Medical Test web app which makes predictions about various diseases using the concept of machine learning.
machine-learning malaria-model pneumonia-model diabetes cancer heart
Language:HTML 188
CBICA / CaPTk
Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
analytics cancer cancer-imaging-research cbica cpp cpp11 cwl cwltool image-analysis itcr machine-learning medical-image-computing medical-image-processing medical-imaging nci nci-itcr nih radiomics radiomics-features u24
Language:C++ 175
kritikaparmar-programmer / HealthCheck
Health Check ✔ is a Machine Learning Web Application made using Flask that can predict mainly three diseases i.e. Diabetes, Heart Disease, and Cancer.
flask machine-learning diabetes-prediction heartdisease cancer-detection python3 jupyter-notebook html css kaggle open-source diabetes heart-disease cancer diseases flutter collaborate student-vscode
Language:Jupyter Notebook 163
greenelab / tybalt
Training and evaluating a variational autoencoder for pan-cancer gene expression data
cancer-genomics deep-learning unsupervised-learning gene-expression variational-autoencoder script tool analysis autoencoder variational-autoencoders cancer
Language:HTML 162
keller-mark / awesome-biological-visualizations
A list of web-based interactive biological data visualizations.
awesome-list awesome visualization data-visualization transcriptomics genomics cancer medicine biology
161
marakeby / pnet_prostate_paper
P-NET, Biologically informed deep neural network for prostate cancer classification and discovery
sparse explainability cancer
Language:HTML 149
OpenGene / MutScan
Detect and visualize target mutations by scanning FastQ files directly
mutation ngs bioinformatics visualization fastq variant detection cancer somatic validation
Language:C 148
Sarek
SciLifeLab / Sarek
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
bioinformatics cancer containers docker genomics germline germline-variants next-generation-sequencing nextflow pipeline reproducible-research reproducible-science singularity somatic somatic-variants workflow
Language:Nextflow 132
greenelab / pancancer
Building classifiers using cancer transcriptomes across 33 different cancer-types
tcga classifier transcriptome pancancer cancer gene-expression machine-learning methodology tool analysis
Language:Jupyter Notebook 118
OpenGene / GeneFuse
Gene fusion detection and visualization
fusion bioinformatics gene alk eml4 ros1 ret cancer cosmic
Language:C 114
AIM-Harvard / SlicerRadiomics
A Slicer extension to provide a GUI around pyradiomics
3d-slicer nciitcr quantitative-imaging nci-itcr radiomics cancer imaging clinical-research
Language:Python 105
ramhiser / datamicroarray
A collection of small-sample, high-dimensional microarray data sets to assess machine-learning algorithms and models.
r cancer colon-cancer high-dimensional-data machine-learning
Language:R 102
sztup / scarHRD
hrd-score genomic-scar-scores wxs cancer hrd-loh telomeric-allelic-imbalances heterozygosity loh
Language:HTML 102
cognoma / cognoma
Putting machine learning in the hands of cancer biologists
philadelphia cancer tcga dataphilly codeforphilly meetup greenelab cognoma
Language:Jupyter Notebook 96
BioDynaMo / biodynamo
BioDynaMo is a high-performance and modular, agent-based simulation platform.
simulation high-performance neuroscience modular-design agent-based agent-based-modelling agent-based-framework biology epidemiology cancer large-scale parallel
Language:C++ 93
PortPy-Project / PortPy
Opensource radiation treatment planning system in Python [AAPM'23]
artificial-intelligence cancer deep-learning dicom mathematical-modelling medical-physics optimization python pytorch radiation-oncology radiotherapy radiation-treatment-planning
Language:Python 90
Bioconductor / GenomicDataCommons
Provide R access to the NCI Genomic Data Commons portal.
tcga nci bioconductor vignette cancer genomics bioinformatics r api-client data-science core-services
Language:R 83
FeTS-AI / Front-End
Federated Learning based Deep Learning. Docs: https://fets-ai.github.io/Front-End/
qt5 cpp cpp11 gui federated-tumor-segmentation fets federated-learning national-institutes cancer cbica
Language:C++ 79
kirbyju / TCIA_Notebooks
Notebooks for working with The Cancer Imaging Archive datasets
cancer dicom imaging tcia-dac
Language:Jupyter Notebook 76
yifengtao / genome-transformer
Predicting multiple cancer phenotypes based on somatic genomic alterations via the genomic impact transformer
transformer gene-embeddings cancer genomic-impact-transformer
Language:Python 76
HyperFoods
luisdrita / HyperFoods
It was built a web application as a step forward in building a 3D recommendation system.
hyperfoods anti-cancer-molecules recipe-retrieval facebook-algorithm ingredients foods imperial recommendation-system deep-learning machine-learning foodreco cancer inverse-cooking recipe1m word2vec svc svm linear-kernel train evaluate
Language:HTML 64
murphycj / AGFusion
Python package to annotate and visualize gene fusions.
gene-fusion protein fusion rna-seq python cancer cancer-genomics chimera bioinformatics structural-variation
Language:Python 59
sigven / cpsr
Cancer Predisposition Sequencing Reporter (CPSR)
cancer-genomics inherited workflow-engine germline-variants cancer-research reporting-tool report-generator docker predisposition cancer-predisposition vcf acmg cancer pathogenicity pathogenic-variants pathogenic-loci genomics-england-panelapp cancer-predisposition-report
Language:R 55
AmpliconSuite / AmpliconSuite-pipeline
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
cancer cancer-genomics ecdna
Language:Python 53
griffithlab / civic-client
Web client for CIViC: Clinical Interpretations of Variants in Cancer
nci-itcr civic javascript front-end-framework cancer cancer-genomics variants
Language:JavaScript 50
sigven / oncoEnrichR
Explore the cancer relevance of your gene list
cancer high-throughput-screening tcga-data report-generator protein-protein-interaction co-expression disease-gene-association crispr-target proteins genesets prioritization protein-complexes cancer-survival functional-enrichment-analysis tissue-enrichment-analysis pathway-enrichment-analysis cancer-hallmark-evidence
Language:R 49
albinsjolin / cancer-whitepaper
Cancer Whitepaper
health healthcare fasting cancer cancer-research
48
KarchinLab / 2020plus
Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
random-forest cancer somatic-variants driver-genes bioinformatics
Language:Python 48
CRI-iAtlas / shiny-iatlas
An interactive web portal for exploring immuno-oncology data. This repo now superseded by iatlas-app
genomics systems-biology immunology cancer
Language:R 47
ding-lab / hotspot3d
3D hotspot mutation proximity analysis tool
mutations perl 3d-proximity proximity-search clustering protein-structure hotspot analysis cancer genomic disease drug ensembl uniprot blat hgnc pymol drugport drugbank
Language:Perl 45