A generative AI extension for JupyterLab

A python extension for quick access to bigWig and bigBed files

This repository contains implementations and illustrative code to accompany DeepMind publications

Sequential regulatory activity predictions with deep convolutional neural networks.

Cloud-native genomic dataframes and batch computing

Significance analysis for clustering single-cell RNA-sequencing data

Python wrapper for MaxEntScan to calculate splice site strength.

An Open Source Machine Learning Framework for Everyone

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

CBAM implementation on Keras

Classification models 1D Zoo - Keras and TF.Keras

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…

Parallel computing with task scheduling

Hyper-parameter optimization for Keras

In-silico Saturation Mutagenesis implementation with 10x or more speedup for certain architectures.

Implementation of binary and categorical/multiclass focal loss using Keras with TensorFlow backend

Interpretation by Deep Generative Masking for Biological Sequences

This repository aims to serve as an index of the work described at Salmen & De Jonghe et. al 2022

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

Latex template for a TUM dissertation/PhD thesis

Splicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data

A deep learning-based tool to identify splice variants

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

A curated and summarized list of bioinformatics bench-marking papers and resources.

A list of interesting genome browser and genome visualization programs

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

Transcriptome-wide network

This is the development home of the workflow management system Snakemake. For general information, see

muon is a multimodal omics Python framework