Integrated Machine Learning for Multi-omics Classification and Prediction

Alpaca dataset from Stanford, cleaned and curated

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

This repository contains implementations and illustrative code to accompany DeepMind publications

Forked from https://github.com/deepmind/deepmind-research/

code for Gogleva et al manuscript

Matilda is a multi-task framework for learning from single-cell multimodal omics data. Matilda leverages the information from the multi-modality of such data and trains a neural network model to si…

Unsupervised neural network for single cell Multi-omics INTegration

A cell-type annotation method for single cell transcriptomics data using semi-supervised learning

Integrative pathway enrichment analysis of multivariate omics data

CellMeSH: Probabilistic Cell-Type Identification Using Indexed Literature.

GeneWalk identifies relevant gene functions for a biological context using network representation learning

Scripts, utilities and programs for genomic bioinformatics.

An accurate GFF3/GTF lift over pipeline

A proof of concept RNA-Seq pipeline with Nextflow

GATK RNA-Seq Variant Calling in Nextflow

data and model repository for single-cell data

Multi-Omics integration and VIsualization in Cancer Subtyping

A comprehensive list of Deep Learning / Artificial Intelligence and Machine Learning tutorials - rapidly expanding into areas of AI/Deep Learning / Machine Vision / NLP and industry specific areas …

TENET is a tool for reconstructing gene regulatory networks from pseudo-time ordered single-cell transcriptomic data.

Statistical power studies for multi-omics experiments.

a pipeline for single cell RNA-seq data analysis

Discovering novel cell types across heterogenous single-cell experiments

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big …

Rmarkdown / compiled html files for human reprogramming dataset analysis

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also…

Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanopore long read sequencing data.