nadeemlab/SPT

Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images

Language: Python - Size: 22.3 MB - Last synced: about 2 hours ago - Pushed: about 17 hours ago - Stars: 22 - Forks: 2

MannLabs/OmicLearn Fork of OmicEra/OmicLearn

🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

Language: Python - Size: 22.2 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 28 - Forks: 6

yiluheihei/microbiomeMarker

R package for microbiome biomarker discovery

Language: R - Size: 23.6 MB - Last synced: 7 days ago - Pushed: 6 months ago - Stars: 162 - Forks: 39

ocbe-uio/DIscBIO

A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics

Language: Jupyter Notebook - Size: 230 MB - Last synced: 6 days ago - Pushed: 6 months ago - Stars: 11 - Forks: 5

MicrobialGenomics-IrsicaixaOrg/dar

dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.

Language: R - Size: 38.5 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 1 - Forks: 0

pranjalpruthi/bhedi

βHΞDI (Biomarker-based Heuristic Engine for Dengue Identification) is a computational tool designed for the identification of Dengue virus serotypes in wastewater next-generation sequencing data.

Language: Go - Size: 6.76 MB - Last synced: 19 days ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0

markwk/awesome-biomarkers

Curated List of Biomarkers, Blood Tests, and Blood Tracking

Size: 275 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 337 - Forks: 24

xinglab-ai/genomap

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)

Language: Python - Size: 43.7 MB - Last synced: 22 days ago - Pushed: 9 months ago - Stars: 9 - Forks: 2

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.

Language: R - Size: 54.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 30 - Forks: 3

lpfann/fri

Python implementation of the feature relevance interval (FRI) algorithm

Language: Python - Size: 15.6 MB - Last synced: 17 days ago - Pushed: over 1 year ago - Stars: 8 - Forks: 4

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.

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CostaLab/CimpleG

CimpleG, an R package to find (small) CpG signatures.

Language: R - Size: 121 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 3 - Forks: 0

amatov/ResistanceBiomarkerAnalysis

Language: MATLAB - Size: 13.2 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

hmarvi/FeatureSelectionOptimizer

Different methods for optimizing state-of-the-art feature selection methods namely SVMRFE, HSICLASSO, and mRMR.

Language: Python - Size: 9.07 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 3 - Forks: 0

XSLiuLab/tumor-immunogenicity-score

TIGS (Tumor Immunogenicity Score) project https://doi.org/10.7554/eLife.49020

Language: R - Size: 306 MB - Last synced: 4 months ago - Pushed: over 2 years ago - Stars: 29 - Forks: 14

euxhenh/phenotype-cover

A package for biomarker selection based on multiset multicover and the cross-entropy-method.

Language: Python - Size: 29.3 KB - Last synced: 16 days ago - Pushed: 10 months ago - Stars: 3 - Forks: 0

KTH-Emil/Venous-thromboembolism-plasma-biomarkers

The following code was used to analyze and vizualise the data in the thesis: "Detecting plasma biomarkers in patients with venous thromboembolism using proximity extension assay"

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PathologyDataScience/HiPS

Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis

Language: Python - Size: 35.2 KB - Last synced: 9 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

ebenasiedu/CM_biomarkers

This repository contains the data and codes used to produce the results and figures in this publication

Language: TeX - Size: 55.2 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 1

SCSE-Biomedical-Computing-Group/SHRED

Code implementation of SHRED variants

Language: Python - Size: 18.2 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 2 - Forks: 0

marchionniLab/OSCC_LN_signature

5 gene pairs for predicting cervical LN metastasis in patients with early-stages oral squamous cell carcinoma

Language: R - Size: 4.01 MB - Last synced: 10 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

aldro61/kover

Learn interpretable computational phenotyping models from k-merized genomic data

Language: Python - Size: 4.38 MB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 50 - Forks: 16

OmicEra/OmicLearn

🧪 🖥 Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

Language: Python - Size: 7.89 MB - Last synced: 12 months ago - Pushed: about 1 year ago - Stars: 52 - Forks: 12

jacobvons/PLCO-paper-data-analysis

Demonstrating machine learning pipeline in biomarker discovery tasks using the PLCO Ovarian Cancer Biomarkers dataset.

Language: Jupyter Notebook - Size: 338 KB - Last synced: 11 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

jaeyunsung/RA_Autoantibodies_2023

Source code and data to reproduce results presented in "Patients with ACPA-positive and ACPA-negative Rheumatoid Arthritis Show Different Serological Autoantibody Repertoires and Autoantibody Associations with Disease Activity" by Cunningham et al. (manuscript submitted for publication).

Language: R - Size: 7.01 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

nhejazi/biotmleData 📦

:package: Bioconductor data package associated with the biotmle R package

Language: R - Size: 74 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

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"

Language: Jupyter Notebook - Size: 6.95 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 2 - Forks: 1

basiralab/FS-Select

FS-Select identifies the best feature selection (FS) method for a given dataset from a pool of FS methods.

Language: Jupyter Notebook - Size: 1.2 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 6 - Forks: 2

basiralab/reproducibleFedGNN

Investigating the reproducibility of federated GNN models

Language: Python - Size: 3.31 MB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 5 - Forks: 2

basiralab/netNorm

We provide both Matlab and Python versions of netNorm. In this folder you find the Maltab version of the code.

Language: MATLAB - Size: 1.31 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 4 - Forks: 0

basiralab/netNorm-PY

netNorm (network normalization) framework for multi-view network integration (or fusion), recoded up in Python by Ahmed Nebli.

Language: Python - Size: 1.14 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 5 - Forks: 2

basiralab/NAGFS

NAG-FS (Network Atlas-Guided Feature Selection) for a fast and accurate graph data classification.

Language: MATLAB - Size: 2.47 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 2 - Forks: 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.

Language: Rich Text Format - Size: 17 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

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

Fall 2020 - Computational Medicine - course project

Language: Jupyter Notebook - Size: 10.9 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

basiralab/NAGFS-PY

NAGFS (Network Atlas-Guided Feature Selection) for a fast and accurate graph data classification code, recoded by Dogu Can ELCI.

Language: Python - Size: 65.4 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 1 - Forks: 2

nhejazi/biotmle

:package: :microscope: R/biotmle: Targeted Learning with Moderated Statistics for Biomarker Discovery

Language: R - Size: 120 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 4 - Forks: 2

AiPBAND/SDAE-biomarkers

Working towards deliverable 5.3

Language: Python - Size: 368 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0