tumor

There are 1 repository under tumor topic.

dellytools / delly
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
structural-variation sv-discovery delly-users delly rearrangement genomic cancer-genomics germline tumor svs
Language:C++ 428
sigven / pcgr
Personal Cancer Genome Reporter (PCGR)
annotation-framework annotation-tool cancer cancer-genomics cancer-variants clinical copy-number-variation interpreter oncology-data precision-cancer-medicine precision-oncology reporting-engine snvs somatic therapeutic-targets tumor variant-interpretation vcf
Language:R 251
digitalcytometry / ecotyper
EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
bulk-rna-seq deconvolution microenvironment single-cell tumor
Language:R 177
guillaumefrd / brain-tumor-mri-dataset
Utilities to download and load an MRI brain tumor dataset with Python, providing 2D slices, tumor masks and tumor classes.
brain classification data dataset detection mri mri-images python segmentation tumor
Language:Jupyter Notebook 93
gatk-workflows / gatk4-somatic-snvs-indels
This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
mutect gatk tumor variants
Language:WDL 76
getzlab / deTiN
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
cancer-genomics cancer-variants cancer-genome-atlas tumor detection tumor-in-normal somatic-mutations tin
Language:Jupyter Notebook 49
marcpaga / sturgeon
Sturgeon is a CNS neural network classifier
classification cns nanopore tumor
Language:Python 30
sustdeeplearning / Liver_And_Tumor_Segmentation_UI
a PyQt5 Implementation
liver tumor segmentation unet pytorch pyqt
Language:Python 25
segmentation-eval
rmsandu / segmentation-eval
Extract and evaluate radiomics for liver cancer tumors from DICOM segmentation masks. Using SimpleITK, PyRadiomics and PyDicom.
dicom segmentation-eval pydicom simpleitk radiomics-feature-extraction tumor pyradiomics ablation segmentation liver-cancer liver-tumor liver-segmentation radiomics-extraction euclidean-distances metrics data-preparation segmentation-masks
Language:Python 23
heavywatal / tumopp
🦀 Tumor growth simulation in C++/R
c-plus-plus simulation tumor r
Language:C++ 19
fepegar / resseg-ijcars
Code, data and model for Pérez-García et al. 2021, "A self-supervised learning strategy for postoperative brain cavity segmentation simulating resections"
medical-image-computing convolutional-neural-networks segmentation tumor epilepsy mri computer-vision
Language:Python 14
xiawei999000 / GBM_PCNSL_CNN_modeling
Deep Learning for Automatic Differential Diagnosis of Primary Central Nervous System Lymphoma and Glioblastoma: Multi-parametric MRI based Convolutional Neural Network Model
multi-parametric-mri deep-learning pcnsl gbm cnn radiomics mp-mri brain tumor
Language:R 13
CSB5 / CaDRReS-Sc
CaDRReS-Sc is a framework for analyzing drug response heterogeneity based on single-cell RNA-seq data
cadrres-sc drug-response-prediction gene-expression-profile scrna-seq tumor
Language:Jupyter Notebook 12
raidionics / Raidionics-Slicer
3D Slicer plugin for automatic segmentation and generation of standardized clinical reports for the most common brain tumors, using MRI volumes
3dslicer medical-imaging mri segmentation tumor
Language:Python 12
aaliyahfiala42 / DATA515-Brain-Scan-Classification
This repository covers a brain scan tumor classification project for the University of Washington DATA 515 course. In our project we train a CNN to predict if a MRI scan (.jpg, .png, .jpeg) is tumorous or not.
machine-learning cnn-keras github-page tumor classification
Language:Python 11
oncodash
oncodash / oncodash
Clinical oncology tumor board decision support system made by the Decider project.
clinical decision-support-system oncology ovarian-cancer selfhosted tumor
Language:Python 11
cgplab / PAMES
Tool to estimate purity of tumor samples exploiting DNA Methylation data
epigenomics dna-methylation admixture purity tumor
Language:R 10
alexcoppe / iWhale
:whale: Dockerized WES pipeline for variants identification in mathced tumor-normal samples
bioinformatics tumor whole-exome-sequencing docker snps indels scons biology genomics
Language:Python 9
ZJUFanLab / CCL-cGPS
A clinical genomics-guided prioritizing strategy enables accurately selecting proper cancer cell lines for biomedical research
cancer ccle cell-lines cosmic gene-expression genomics kolmogorov-smirnov nci60 ranking-algorithm subtype tcga tumor
Language:R 9
broadinstitute / celligner
tumor - cancer cell line alignment. Use it on the depmap portal or install it with pip.
genomics tumor cancer alignement celligner rnaseq
Language:Jupyter Notebook 7
GianlucaPorcelli / MRI_toumor_segmentation
The work presented explains how to segment the brain tumour area in absence of interaction with user basing his technique on a saliency map constructed from three different resonance techniques.
adaptive gbm glioblastoma matlab mri-images pseudocolor salience saliency saliency-map superpixel-segmentation superpixels threshold thresholding tumor tumor-segmentation
Language:MATLAB 7
renatopuga / somatico
GATK 4 Mutect2 Somático
gatk4 mutect2 pon somatic-variants gitpod colab-notebook hg19 normal tumor vep
Language:Shell 7
marianocabezas / challenges2017
Repository with models, experiments and approaches for the BraTS 2017 and iSeg segmentation challenges.
cnn-model brats challenge tumor segmentation
Language:Python 6
neuronets / ams
Automated meningioma segmentation
segmentation trained-models tensorflow neuroimaging mri tumor tumor-segmentation
Language:Python 6
AryanFelix / Brain-Tumor-Classification
A Brain Tumor Classification and Segmentation tool to easily detect from Magnetic Resonance Images or MRI. It works on a Convolutional Neural Network created using Keras.
tensorflow keras cnn classification segmentation brain tumor brain-tumor-segmentation brain-tumor-classification
Language:Jupyter Notebook 5
tharunchitipolu / Breast-cancer-prediction-using-machine-learning
predict whether the tumor is Malignant or Benign.
breast-cancer-prediction machine-learning prediction python python3 tensorflow tumor wisconsin
Language:Jupyter Notebook 5
agam1092005 / Brain_Tumor_Classifier
Predicting & Classifying Brain tumor using CNN model
deep-learning machine-learning classification cnn-model image-classification image-processing keras mlproject neural-network prediction python3 tensorflow cancer health healthcare tumor tumor-detection
Language:Jupyter Notebook 4
aysekonus / BrainTumorSegmentation
"Derin Öğrenme Teknolojisi ile Beyin Tümörü Tespiti ve Segmentasyonu" konusu ele alınmış olup, tümörü kolaylıkla ve yüksek doğrulukta tespit edebilen bir bilgisayar destekli tümör tespit sistemi geliştirilmiştir.
brain brain-tumor brain-tumor-segmentation deep-learning deep-neural-networks derin-ogrenme mask-rcnn resnet resnet-101 t tumor tumor-detection tumor-segmentation
Language:Jupyter Notebook 4
CCBR / METRO
Mouse nEoanTigen pRedictOr
bioinformatics mouse neoantigen-prediction neoepitopes tumor vaccine
Language:Python 4
cit-bioinfo / WISP
Weighted In Silico Pathology: a novel approach to assess intra-tumoral heterogeneity
deconvolution genomics tumor heterogeneity transcriptomics methylation cancer
Language:R 4
rahmanidashti / PPINetworkAnalysis
Comparison of Tumor and Normal Cells Protein-Protein Interaction Network Parameters
network-science complex-networks network-analysis protein-protein-interaction graph centrality tumor cell
Language:R 4
Adl1coder / ImageProcessingExercises
image processing exercises with google colab
google-colab histogram histogram-equalization image-processing matplotlib opencv python3 brain brain-tumor-detection detection tumor kaggle mri mri-brain
Language:Jupyter Notebook 3
andreped / neukit
:hugs: neukit: web application for automatic brain extraction and preoperative tumor segmentation from MRI
deep-learning demo huggingface meningioma mri pretrained segmentation spaces t1 web-app brain brain-extraction glioma metastasis tumor high-grade low-grade raidionics
Language:Python 3
heavywatal / rtumopp
🦀 R interface to tumopp
rcpp simulation tumor
Language:R 3
Ksuryateja / BrainTumorDetector
Building a detection model using a convolutional neural network in Keras.
dataset convolutional-neural-network augmented-data tumor detection-model python keras-tensorflow
Language:Jupyter Notebook 3
mingrui / GenerateObj
A 3D Slicer Module that 1. uses ROBEX brain extraction to generate mesh.obj; 2. tumor label mask to mesh.obj
3d slicer unity3d nifti obj medical brain tumor visualization
Language:Python 3

tumor

dellytools / delly

sigven / pcgr

digitalcytometry / ecotyper

guillaumefrd / brain-tumor-mri-dataset

gatk-workflows / gatk4-somatic-snvs-indels

getzlab / deTiN

marcpaga / sturgeon

sustdeeplearning / Liver_And_Tumor_Segmentation_UI

rmsandu / segmentation-eval

heavywatal / tumopp

fepegar / resseg-ijcars

xiawei999000 / GBM_PCNSL_CNN_modeling

CSB5 / CaDRReS-Sc

raidionics / Raidionics-Slicer

aaliyahfiala42 / DATA515-Brain-Scan-Classification

oncodash / oncodash

cgplab / PAMES

alexcoppe / iWhale

ZJUFanLab / CCL-cGPS

broadinstitute / celligner

GianlucaPorcelli / MRI_toumor_segmentation

renatopuga / somatico

marianocabezas / challenges2017

neuronets / ams

AryanFelix / Brain-Tumor-Classification

tharunchitipolu / Breast-cancer-prediction-using-machine-learning

agam1092005 / Brain_Tumor_Classifier

aysekonus / BrainTumorSegmentation

CCBR / METRO

cit-bioinfo / WISP

rahmanidashti / PPINetworkAnalysis

Adl1coder / ImageProcessingExercises

andreped / neukit

heavywatal / rtumopp

Ksuryateja / BrainTumorDetector

mingrui / GenerateObj