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gatk4 RNA variant calling pipeline

Nextflow 45 37 Updated Apr 1, 2025

Making Protein Design accessible to all via Google Colab!

Python 704 158 Updated Mar 28, 2025

A comprehensive cancer DNA/RNA analysis and reporting pipeline

Nextflow 63 17 Updated Apr 3, 2025

Making RNA-based models accessible to all.

Jupyter Notebook 8 1 Updated Feb 15, 2025

A new markup-based typesetting system that is powerful and easy to learn.

Rust 38,780 1,069 Updated Apr 2, 2025

Python package for the semi-supervised analysis of multi-omics data

Python 6 Updated Jan 27, 2025

Protein 3D structure prediction pipeline

Nextflow 77 55 Updated Mar 28, 2025

AlphaFold 3 inference pipeline.

Python 6,308 785 Updated Mar 24, 2025

Genome-scale protein function classification

Java 320 69 Updated Apr 2, 2025

Seamless R and C++ Integration

C++ 755 218 Updated Mar 31, 2025
C 28 10 Updated Dec 1, 2022

Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework

Perl 22 8 Updated Nov 29, 2022

Biodiversity Genomics Academy 2023: Aligning whole genomes using Cactus

2 1 Updated Sep 29, 2023

MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.

Python 50 28 Updated Sep 12, 2019

Hierarchical Alignment Format

C++ 167 39 Updated Dec 30, 2024

Tools for manipulating biological data, particularly multiple sequence alignments

Python 155 54 Updated Sep 15, 2024

Leaflet is a probabilistic model that identifies latent cell states defined by splicing changes.

Jupyter Notebook 10 1 Updated May 10, 2024

RNA-seq Quantification of Alternative Polyadenylation

Python 46 10 Updated Jun 16, 2023

A collection of modern/faster/saner alternatives to common unix commands.

31,807 797 Updated Sep 10, 2024

nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.

Nextflow 3 9 Updated Mar 26, 2025

Tools to reproduce the steps to run nf-core pipelines for bioinformatics analysis within Linux environments.

Python 1 Updated Apr 26, 2022

Machine Learning-based tool to assess the functional relevance of splice isoforms.

Python 10 1 Updated Feb 8, 2023

Source code of the R packge BgeeDB to use data from the Bgee database

R 16 6 Updated Feb 3, 2025

Python library to handle Gene Ontology (GO) terms

Python 814 211 Updated Nov 9, 2024

Neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data

Python 44 4 Updated Feb 28, 2025

A script to make Jsons with Alphafold3

Python 5 Updated Mar 4, 2025

A script to make downloading of SRA/GEO data easier

Python 30 10 Updated Oct 6, 2023

Scripts associated to transcriptome-wide analysis of the effects of systematic knock down of splicing factors and regulators using siRNAs in HeLa cells

R 7 Updated Jan 8, 2025

During brain development, neural stem cells (NSCs) undergo multiple fate-switches to generate various neuronal subtypes and glial cells, exhibiting distinct transcriptomic profiles at different sta…

R 2 1 Updated Jul 9, 2021

Code and data associated with the PastDB publication (Martin et al, 2021).

Perl 3 1 Updated Jan 23, 2021
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