Stars
An R package to process and analyze transcriptomic data
Tool for plotting sequencing data along genomic coordinates.
This package provides a function to reformat lists of genome coverage files, such as bigWig of bam files, into the directory structure of a UCSC Track Hub ready to be visualized in the genome brows…
a framework for training sequence-level deep learning networks
CADD-SV – a framework to score the effect of structural variants
Tokenizers and Machine Learning Models for biological sequence data
Interactive deep learning book with multi-framework code, math, and discussions. Adopted at 500 universities from 70 countries including Stanford, MIT, Harvard, and Cambridge.
The fastai book, published as Jupyter Notebooks
Toolset for SV simulation, comparison and filtering
MetaDome is aimed at professionals in the (bio-)medical field of human genetics who wish to visualize the position of their mutation of interest in the context of general population-based genetic …
deep residual neural network for classifying the pathogenicity of missense mutations.
structural variant calling and genotyping with existing tools, but, smoothly.
Viola is a flexible and powerful python package designed specifically for analysis of genomic structural variant (SV) signatures.
The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
Category-wide association study (CWAS) (Werling et al., 2018; An et al., 2018)
MuRaL is a deep learning framework for building base-resolution mutation rate maps.
Elucidating the Utility of Genomic Elements with Neural Nets
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
List of gene lists for genomic analyses.
Official code repository for GATK versions 4 and up