biomarker-discovery

There are 2 repositories under biomarker-discovery topic.

markwk / awesome-biomarkers
Curated List of Biomarkers, Blood Tests, and Blood Tracking
blood blood-test vitamin quantified quantified-self blood-tracking awesome awesome-list biomarkers biomarker-discovery
346
yiluheihei / microbiomeMarker
R package for microbiome biomarker discovery
microbiome biomarker-discovery lefse metagenomics r differential-abundance-analysis r-package
Language:R 162
OmicEra / OmicLearn
🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data
bioinformatics biomarker-discovery machine-learning omics proteomics
Language:Python 58
aldro61 / kover
Learn interpretable computational phenotyping models from k-merized genomic data
machine-learning genomics k-mer biomarker-discovery phenotypes
Language:Python 50
OmicSelector
kstawiski / OmicSelector
OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic tool development from high-throughput high-throughput omics experiments and other multidimensional datasets. Initially developed for miRNA-seq, RNA-seq and qPCR.
bioinformatics bioinformatics-pipeline biomarker-discovery biomarkers classification data-mining data-science deep-learning deep-neural-networks docker-image feature-selection mirna neural-network next-generation-sequencing omics qpcr r r-package rna-seq variable-selection
Language:R 30
XSLiuLab / tumor-immunogenicity-score
TIGS (Tumor Immunogenicity Score) project https://doi.org/10.7554/eLife.49020
analysis-report reproducible-analysis manuscript tumor-immunogenicity immunotherapy biomarker-discovery
Language:R 30
MannLabs / OmicLearn
🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data
bioinformatics biomarker-discovery machine-learning omics proteomics transcriptomics
Language:Python 29
nadeemlab / SPT
Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images
biomarker-discovery spatial-analysis tumor-microenvironment clinical-workflow image-analysis python single-cell-analysis
Language:Python 22
PathologyDataScience / HiPS
Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis
biomarker-discovery biomedical-image-processing breast-cancer computational-pathology digital-pathology survival-prediction explainable-ai
Language:Python 15
nostalgia-cnt / vibe
👀 An all-purpose eye tracking web application and API for Alzheimer's disease research (3 tasks, <3 mins). 1st place in the 2021 CNT hackathon https://www.cnthackathon.org/
eye-tracking eye-detection eyegazer eye alzheimers-disease alzheimer-disease-diagnostics alzheimer eyetracking biometrics biomarker-discovery alzheimer-disease alzheimer-dementia alzheimers
Language:JavaScript 11
ocbe-uio / DIscBIO
A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics
transcriptomics biomarker-discovery single-cell-analysis scrna-seq jupyter-notebook r-package
Language:Jupyter Notebook 11
xinglab-ai / genomap
Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)
bioinfomatics-pipeline bioinformatics bioinformatics-tool deep-learning genomic-data-analysis genomics genomics-visualization single-cell tabular-data biomarker-discovery biomarkers classification-algorithm data-classification multi-omic-integration regression-algorithms trajectory-inference visualization cell-annotation
Language:Python 10
basiralab / reproducibleFedGNN
Investigating the reproducibility of federated GNN models
biomarker-discovery brain-connectome brain-graph brain-network classification computer-aided-diagnosis decentralized-learning deep-learning feature-selection federated-learning federation geometric-deep-learning gnn graph-neural-networks interpretable-ai reproducibility reproducible-science brain-diagnosis model-reproducibility
Language:Python 8
fri
lpfann / fri
Python implementation of the feature relevance interval (FRI) algorithm
scikit-learn feature-selection machine-learning-algorithms bioinformatics python biomarker-discovery feature-relevance-interval data-science
Language:Python 8
basiralab / FS-Select
FS-Select identifies the best feature selection (FS) method for a given dataset from a pool of FS methods.
feature-selection machine-learning reproducibility biomarker-discovery brain-networks brain-disorders pattern-recognition classification
Language:Jupyter Notebook 6
basiralab / netNorm
We provide both Matlab and Python versions of netNorm. In this folder you find the Maltab version of the code.
network-fusion network-normalization network-integration sample-selection high-order-networks brain-connectivity network-neuroscience biomarker-discovery multi-view-networks multigraph-integration multigraph-fusion machine-learning connectome-mapping brain-disorders
Language:MATLAB 5
basiralab / netNorm-PY
netNorm (network normalization) framework for multi-view network integration (or fusion), recoded up in Python by Ahmed Nebli.
network-fusion network-normalization network-integration sample-selection brain-connectivity network-neuroscience biomarker-discovery multi-view-networks multigraph-integration multigraph-fusion connectome-mapping brain-networks high-order-connectivity brain-disorders
Language:Python 5
fuad021 / biomarker-identification
This repository is the author implementation of the paper "Biomarker Identification by Reversing the Learning Mechanism of Autoencoder and Recursive Feature Elimination"
biomarker-discovery bioinformatics gene-expression
Language:Jupyter Notebook 5
CimpleG
CostaLab / CimpleG
CimpleG, an R package to find (small) CpG signatures.
methylation deconvolution cpg-signature biomarker-discovery biomarkers cell-type-classification r
Language:R 4
nhejazi / biotmle
:package: :microscope: R/biotmle: Targeted Learning with Moderated Statistics for Biomarker Discovery
bioconductor bioconductor-package bioconductor-packages bioinformatics biomarker-discovery biostatistics causal-inference computational-biology machine-learning r statistics targeted-learning
Language:R 4
euxhenh / phenotype-cover
A package for biomarker selection based on multiset multicover and the cross-entropy-method.
biomarker biomarker-discovery genes scrna-seq set-cover
Language:Python 3
hmarvi / FeatureSelectionOptimizer
Different methods for optimizing state-of-the-art feature selection methods namely SVMRFE, HSICLASSO, and mRMR.
feature-selection gene-expression machine-learning python data-analysis biomarker-discovery machine-learning-algorithms clustering
Language:Python 3
SCSE-Biomedical-Computing-Group / SHRED
Code implementation of SHRED variants
adhd autism biomarker-discovery data-harmonisation disease-classification fmri schizophrenia
Language:Python 3
basiralab / NAGFS
NAG-FS (Network Atlas-Guided Feature Selection) for a fast and accurate graph data classification.
network-atlas network-fusion network-integration graph-fusion graph-classification feature-selection brain-connectivity biomarker-discovery graph-representation graph-template-learning network-neuroscience brain-disorder computer-aided-diagnosis
Language:MATLAB 2
himelmallick / Bayes_Review_ASA_BIOP
This repository houses all the analysis codes described in the Bayesian nonclinical review paper published in Communications in Statistics – Case Studies and Data Analysis.
bayesian-inference biomarker-discovery biostatistics machine-learning statistics
Language:HTML 2
AiPBAND / SDAE-biomarkers
Working towards deliverable 5.3
stacked-denoising-autoencoders paper biomarker-discovery latent-semantic-analysis latent-representations journal
Language:Python 1
anjanatiha / Distributed-Machine-Learning-for-Bio-marker-Detection-from-Wearable-Sensor-Big-Data
Distributed Machine Learning for Bio-marker Prediction from Big Data Stream collected from Multi-modal Wearable Sensor Data
machine-learning predictive-analytics distributed-computing sensor-data apache-spark mhealth mobile-health biomarker-discovery distributed-training
Language:Python 1
ashmitan / DeepLearningInHealthcare
Objective of this project is to compare different machine learning models and deep learning neural networks. It also focusses on hyperparameter tuning and performance of deep learning neural network over machine learning. Dataset Used: Diabetes prediction
deep-learning diabetes-prediction machine-learning biomarker-discovery healthcare tensorflow artificial-neural-networks
Language:Jupyter Notebook 1
basiralab / NAGFS-PY
NAGFS (Network Atlas-Guided Feature Selection) for a fast and accurate graph data classification code, recoded by Dogu Can ELCI.
network-atlas network-fusion network-integration graph-fusion network-neuroscience brain-connectivity feature-selection biomarker-discovery graph-representation graph-template-learning graph-classification brain-disorder
Language:Python 1
jaeyunsung / RA_Autoantibodies_2023
biomarker-discovery rheumatoid-arthritis serology autoantibodies
Language:R 1
MicrobialGenomics-IrsicaixaOrg / dar
dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.
microbiome microbiology rstats bioconductor biomarker-discovery differential-abundance-analysis feature-selection phyloseq
Language:R 1
ryanquinnnelson / CMU-02718-Biomarker-Discovery-using-ML
Fall 2020 - Computational Medicine - course project
biomarker-discovery immunological-data machine-learning anova mutual-information svm kmeans-clustering recursive-feature-elimination random-forest-classifier
Language:Jupyter Notebook 1
ebenasiedu / CM_biomarkers
This repository contains the data and codes used to produce the results and figures in this publication
biomarker-discovery malaria malaria-diagnosis transcriptomics
Language:TeX 0
jacobvons / PLCO-paper-data-analysis
Demonstrating machine learning pipeline in biomarker discovery tasks using the PLCO Ovarian Cancer Biomarkers dataset.
biomarker-discovery machine-learning
Language:Jupyter Notebook 0
sermare / carP-encoding-a-Ca2--regulated-putative-phytase
Here, we studied the conservation of carP sequence and its occurrence in diverse phylogenetic groups of bacteria. In silico analysis revealed that carP and its two paralogues PA2017 and PA0319 are primarily present in P. aeruginosa and belong to the core genome of the species.
biomarker-discovery pseudomonas cystic-fibrosis calcium-network sequence-conservation putative-phytase
Language:Rich Text Format 0
amatov / ResistanceBiomarkerAnalysis
biomarker-discovery circulating-tumor-cells drug-response-prediction breast-cancer gastric-cancer prostate-cancer circular-hough-transform voronoi-diagram intensity-histogram-thresholding stationary-wavelet-transform sobel-filter feature-eccentricity difference-of-gaussian tubulin-bundling tubulin-inhibitors tubulin-tyrosination microfluidics-chip-enrichment brca1-drug-resistance paclitaxel-therapy transcription-factor-localization
Language:MATLAB

biomarker-discovery

markwk / awesome-biomarkers

yiluheihei / microbiomeMarker

OmicEra / OmicLearn

aldro61 / kover

kstawiski / OmicSelector

XSLiuLab / tumor-immunogenicity-score

MannLabs / OmicLearn

nadeemlab / SPT

PathologyDataScience / HiPS

nostalgia-cnt / vibe

ocbe-uio / DIscBIO

xinglab-ai / genomap

basiralab / reproducibleFedGNN

lpfann / fri

basiralab / FS-Select

basiralab / netNorm

basiralab / netNorm-PY

fuad021 / biomarker-identification

CostaLab / CimpleG

nhejazi / biotmle

euxhenh / phenotype-cover

hmarvi / FeatureSelectionOptimizer

SCSE-Biomedical-Computing-Group / SHRED

basiralab / NAGFS

himelmallick / Bayes_Review_ASA_BIOP

AiPBAND / SDAE-biomarkers

anjanatiha / Distributed-Machine-Learning-for-Bio-marker-Detection-from-Wearable-Sensor-Big-Data

ashmitan / DeepLearningInHealthcare

basiralab / NAGFS-PY

jaeyunsung / RA_Autoantibodies_2023

MicrobialGenomics-IrsicaixaOrg / dar

ryanquinnnelson / CMU-02718-Biomarker-Discovery-using-ML

ebenasiedu / CM_biomarkers

jacobvons / PLCO-paper-data-analysis

sermare / carP-encoding-a-Ca2--regulated-putative-phytase

amatov / ResistanceBiomarkerAnalysis