A powerful abstraction of gene databases

An open platform which provides information about miRNAs and genes from different popular databases

Single cell Nanopore sequencing data for Genotype and Phenotype

A research biochemical network explorer and genetic cytohistological encyclopedia.

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

A comprehensive quality-control and quantification RNA-seq pipeline

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

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

RNA-Seq Pipeline for processing paired-end FASTQ transcripts generated from Illumina sequencing. The pipeline trims adapter sequences, aligns transcripts to a specified region of interest on the reference genome, and facilitates downstream analysis.

Sobolev alignment of deep probabilistic models for comparing single cell profiles

Differential Dependency Network

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

Code for the ExpectoSC model

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

Transcripts annotation and GO enrichment Fisher tests

Variational Auto-Encoder that generates synthetic gene expression data

Roche entry into Precision FDA hackathon

Description of the emQTL analysis related to the paper "Epigenetic alterations at distal enhancers are linked to proliferation in human breast cancer".

Predicting gene expression using promoter sequence.