microbiome
gut-microbiome-allergy-data
Dataset Card for Gut Microbiome–Food Allergy Prediction Datasets
Dataset Summary
This repository contains multiple human gut microbiome datasets curated for predicting food allergy development.
Each dataset corresponds to a distinct cohort with longitudinal microbiome sampling, providing both metadata and derived embeddings suitable for machine learning.
The datasets are designed to support binary classification of subjects into healthy vs allergic categories, enabling… See the full description on the dataset page: https://huggingface.co/datasets/hugging-science/gut-microbiome-allergy-data.qiime2_antibiotic_microbiome_analysis
Soil Microbiome Responses to Antibiotic Contamination: A Dual-Marker Amplicon Analysis
Overview
This repository contains a fully reproducible computational pipeline for the analysis of soil microbial community responses to escalating antibiotic concentrations. The study employs a dual-marker amplicon sequencing approach, simultaneously profiling bacterial communities via the 16S rRNA gene (V3-V4 region) and fungal communities via the internal transcribed spacer… See the full description on the dataset page: https://huggingface.co/datasets/QasimHussain/qiime2_antibiotic_microbiome_analysis.Human_Gut_Microbiome_Atlas
Deep Metagenomics of the Human Gut Microbiome in IBD: A Multi-Omics Data Atlas
A curated longitudinal dataset and computational framework for dissecting the temporal ecology of Inflammatory Bowel Disease (IBD).
Abstract
This project presents a comprehensive, high-resolution computational analysis of the human gut microbiome in Inflammatory Bowel Disease (IBD), leveraging deep metagenomic sequencing data from the HMP2 (Integrative Human Microbiome Project)… See the full description on the dataset page: https://huggingface.co/datasets/QasimHussain/Human_Gut_Microbiome_Atlas.colorectal-carcinoma-microbiome-fengqThe dataset contains 16S rRNA gene sequencing data from healthy controls and colorectal cancer patients. The dataset was used in the paper "Gut microbiome development along the colorectal adenoma-carcinoma sequence" by Feng et al. (2015).bio-faiss-microbiome-v1
bio-faiss-microbiome-v1
A FAISS index + metadata for scientific retrieval
Contents
index.faiss: FAISS index (cosine w/ inner product).
meta.jsonl: one JSON per chunk; fields include chunk_id, paper_id, title, section, subsection, paragraph_index, keywords, boost.
Build provenance
Chunking: hierarchical (section→paragraph→~380-token chunks, ~15% overlap)
Embedder: bio-protocol/scientific-retriever (mean-pooled, L2-normalized)
Similarity: cosine via inner… See the full description on the dataset page: https://huggingface.co/datasets/bio-protocol/bio-faiss-microbiome-v1.Human_Gut_Microbiome_Data
Human Gut Microbiome Dataset (40-class)
Pre-processed, train/val/test-split human gut microbiome dataset used to train and evaluate
MicrobiomeFM, a Transformer-based foundation model for multi-class disease classification
from shotgun metagenomic data.
This release contains the 40-class filtered version of the dataset that the published
results were obtained on (test accuracy ≈ 96.05%, weighted F1 ≈ 0.950, macro F1 ≈ 0.691).
It is derived from the curatedMetagenomicData (cMD)… See the full description on the dataset page: https://huggingface.co/datasets/mohitraiyani27/Human_Gut_Microbiome_Data.