Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
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Updated
Mar 30, 2024 - Python
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
Deep learning for gene expression inference
CodonTransformer: The ultimate tool for codon optimization, optimizing DNA sequences for heterologous protein expression across 164 species.
A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
Fast visualization tool for large-scale and high dimensional single-cell data
Data and code related to the paper "ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa..." Jie Tan, et al · mSystems · 2016
This repository contains the python package for Helical
Single cell Nanopore sequencing data for Genotype and Phenotype
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biological information"
The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
scripts for RNA-Seq analysis
Transcripts annotation and GO enrichment Fisher tests
GEDFN: Graph-Embedded Deep Feedforward Network
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
Variational Auto-Encoder that generates synthetic gene expression data
Survival Prediction for Gastric Cancer via Multimodal Learning of Whole Slide Images and Gene Expression -- BIBM 2022
Predictive models and analysis of cancer prognosis and drug response using primary tumor microbial abundances derived from WGS and RNA-seq sequencing data for 32 TCGA cancers (Poore et al. Nature 2020), including equivalent models using TCGA RNA-seq gene expression and combined microbial abundance and gene expression for comparison.
MYB transcription factors are one of the largest gene family in plants and control many processes. This repository provides additional background to the #MYB_Monday tweets
MR-link and genome integration. genome_integration is a repository for the analysis of genomic data. Specifically, the repository implements the causal inference method MR-link, as well as other Mendelian randomization methods.
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