Stars
LIVI is an interpretable deep learning framework that enables trans-eQTL mapping at single-cell resolution.
A scikit-learn-compatible library for estimating prediction intervals and controlling risks, based on conformal predictions.
D3.js based visualizations of cobrapy metabolic models
The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation
R package for "sum of single effects" regression.
This study benchamrked the performance of existing cell deconvolution methods with human brain transcriptome and evaluated the biological applications of deconvoluted data in eQTL mapping and diffe…
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
Integrative Analyses across 388 human brain samples at single-cell resolution
The generic genome-scale metabolic model of Homo sapiens
scikit-learn: machine learning in Python
A scikit-learn compatible neural network library that wraps PyTorch
Sparse graph recovery by optimizing deep unrolled networks (unsupervised-GLAD)
A container (S4 class) for matrix-like assays
Notebooks accompanying the paper "Navigating the pitfalls of applying machine learning in genomics"
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
An opinionated list of Python frameworks, libraries, tools, and resources
A quality control analysis tool for high throughput sequencing data
Quantify and interpret divers of variation in multilevel gene expression experiments
Foundation of integer range manipulation in Bioconductor
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in Python using Scikit-Learn, Keras and TensorFlow 2.