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++ 443
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 254
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 184
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.
data dataset mri mri-images brain classification segmentation detection tumor python
Language:Jupyter Notebook 95
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This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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.
gatk mutect 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 32
sustdeeplearning / Liver_And_Tumor_Segmentation_UI
a PyQt5 Implementation
liver pyqt pytorch segmentation tumor unet
Language:Python 27
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 24
heavywatal / tumopp
🦀 Tumor growth simulation in C++/R
c-plus-plus r simulation tumor
Language:C++ 19
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 14
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"
computer-vision convolutional-neural-networks epilepsy medical-image-computing mri segmentation tumor
Language:Python 14
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 14
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 13
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
brain cnn deep-learning gbm mp-mri multi-parametric-mri pcnsl radiomics tumor
Language:R 13
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
cgplab / PAMES
Tool to estimate purity of tumor samples exploiting DNA Methylation data
admixture dna-methylation epigenomics purity tumor
Language:R 10
alexcoppe / iWhale
:whale: Dockerized WES pipeline for variants identification in mathced tumor-normal samples
bioinformatics biology docker genomics indels scons snps tumor whole-exome-sequencing
Language:Python 9
ZJUFanLab / CCL-cGPS
A clinical genomics-guided prioritizing strategy enables accurately selecting proper cancer cell lines for biomedical research
cancer cell-lines ccle tcga nci60 cosmic tumor subtype genomics gene-expression kolmogorov-smirnov ranking-algorithm
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.
brats challenge cnn-model segmentation tumor
Language:Python 6
neuronets / ams
Automated meningioma segmentation
mri neuroimaging segmentation tensorflow trained-models tumor tumor-segmentation
Language:Python 6
tharunchitipolu / Breast-cancer-prediction-using-machine-learning
predict whether the tumor is Malignant or Benign.
breast-cancer-prediction tumor machine-learning prediction wisconsin tensorflow python python3
Language:Jupyter Notebook 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
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 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
CCBR / METRO
Mouse nEoanTigen pRedictOr
bioinformatics neoantigen-prediction mouse tumor vaccine neoepitopes
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 tumor simulation
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 brain medical nifti obj slicer tumor unity3d 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

CSB5 / CaDRReS-Sc

fepegar / resseg-ijcars

raidionics / Raidionics-Slicer

oncodash / oncodash

xiawei999000 / GBM_PCNSL_CNN_modeling

aaliyahfiala42 / DATA515-Brain-Scan-Classification

cgplab / PAMES

alexcoppe / iWhale

ZJUFanLab / CCL-cGPS

broadinstitute / celligner

GianlucaPorcelli / MRI_toumor_segmentation

renatopuga / somatico

marianocabezas / challenges2017

neuronets / ams

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

AryanFelix / Brain-Tumor-Classification

aysekonus / BrainTumorSegmentation

agam1092005 / Brain_Tumor_Classifier

CCBR / METRO

cit-bioinfo / WISP

rahmanidashti / PPINetworkAnalysis

Adl1coder / ImageProcessingExercises

andreped / neukit

heavywatal / rtumopp

Ksuryateja / BrainTumorDetector

mingrui / GenerateObj