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Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
Fast and modular sklearn replacement for generalized linear models
Compressing protein structures effectively with torsion angles
Software for the visualization of sequence-function relationships
Interactive 2D scatter plot widget for Jupyter Lab and Notebook. Scales to millions of points!
A neural network framework for researchers studying acoustic communication
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
Demonstrate how to structure a project, build Python packages, unit testing, GitHub Actions, Read the Docs (RTD), package managers, distributions, containers, and high performance computing (HPC).
Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
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🏆 A ranked list of awesome machine learning Python libraries. Updated weekly.
A curated list of awesome Bioinformatics libraries and software.
Notebooks accompanying the paper "Navigating the pitfalls of applying machine learning in genomics"
Fast alignment and preprocessing of chromatin profiles
Efficient pythonic random access to fasta subsequences
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Set up your GitHub Actions workflow with a specific version of Python
In-silico Saturation Mutagenesis implementation with 10x or more speedup for certain architectures.
Wolfram Mathematica distributions parser for pomegranate
Python package for efficient mass spectrometry data processing and visualization
A great intro dataset for data exploration & visualization (alternative to iris).
Beyond Accuracy: Behavioral Testing of NLP models with CheckList