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A new markup-based typesetting system that is powerful and easy to learn.
Python package for the semi-supervised analysis of multi-omics data
Genome-scale protein function classification
Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework
Biodiversity Genomics Academy 2023: Aligning whole genomes using Cactus
MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.
Tools for manipulating biological data, particularly multiple sequence alignments
Leaflet is a probabilistic model that identifies latent cell states defined by splicing changes.
RNA-seq Quantification of Alternative Polyadenylation
A collection of modern/faster/saner alternatives to common unix commands.
nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.
Tools to reproduce the steps to run nf-core pipelines for bioinformatics analysis within Linux environments.
Machine Learning-based tool to assess the functional relevance of splice isoforms.
Source code of the R packge BgeeDB to use data from the Bgee database
Python library to handle Gene Ontology (GO) terms
Neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data
A script to make downloading of SRA/GEO data easier
Scripts associated to transcriptome-wide analysis of the effects of systematic knock down of splicing factors and regulators using siRNAs in HeLa cells
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…
Code and data associated with the PastDB publication (Martin et al, 2021).
RPHAST: Phylogenetic Analysis with Space/Time Models in R
A neural network model to predict splice site usage and splicing-altering mutations
Download and parse data from Garmin Connect or a Garmin watch, FitBit CSV, and MS Health CSV files into and analyze data in Sqlite serverless databases with Jupyter notebooks.