jmschrei / avocado
Avocado is a multi-scale deep tensor factorization model that learns a latent representation of the human epigenome and enables imputation of epigenomic experiments that have not yet been performed.
☆118Updated 3 years ago
Alternatives and similar repositories for avocado:
Users that are interested in avocado are comparing it to the libraries listed below
- TF MOtif Discovery from Importance SCOres☆135Updated last year
- Model zoo for genomics☆166Updated 8 months ago
- Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit☆49Updated last year
- A simple pythonic interface to biomart.☆55Updated 5 years ago
- GeneWalk identifies relevant gene functions for a biological context using network representation learning☆130Updated 8 months ago
- Downloader for ENCODE☆32Updated 4 years ago
- Python biomart API☆65Updated last year
- Simple and efficient access to genomic data for deep learning models.☆43Updated 5 years ago
- ☆84Updated 4 years ago
- Python implementation of the Loom file format - http://loompy.org☆142Updated 4 months ago
- Tissue-specific variant effect predictions on splicing☆42Updated last year
- Annotation of genomic regions using transcription factor binding sites and epigenetic data☆40Updated 2 years ago
- Deep Feature Interaction Maps (DFIM)☆53Updated 6 years ago
- easy access to benchmark datasets☆50Updated 6 years ago
- predicting expression effects of human genome variants ab initio from sequence☆127Updated 2 months ago
- Tools for working with BUS files☆95Updated 5 months ago
- Porting DESeq2 into python via rpy2☆68Updated last year
- Linear mixed model for genomic analyses.☆104Updated 3 years ago
- Notebooks accompanying the paper "Navigating the pitfalls of applying machine learning in genomics"☆45Updated last year
- Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.☆114Updated 5 months ago
- Standard set of data-loaders for training and making predictions for DNA sequence-based models.☆81Updated 7 months ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆71Updated last month
- scMatch: a single-cell gene expression profile annotation tool using reference datasets☆24Updated 3 years ago
- Concise: Keras extension for regulatory genomics☆35Updated 2 years ago
- Deep-learning Augmented RNA-seq analysis of Transcript Splicing☆111Updated last year
- Elucidating the Utility of Genomic Elements with Neural Nets☆69Updated 4 months ago
- Parsing tools for GTF (gene transfer format) files☆119Updated last month
- A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.☆87Updated 5 years ago
- BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/pa…☆83Updated 10 months ago
- pysster: Learning Sequence And Structure Motifs In Biological Sequences Using Convolutional Neural Networks☆86Updated 5 years ago