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80 search results found

Dna Diffusion ⭐ 297

🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

Ideogram ⭐ 265

Chromosome visualization for the web

Dragonn ⭐ 245

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

Comp Genomics Class ⭐ 236

Code and examples for JHU Computational Genomics class

Kipoi's model zoo API

Deep learning infrastructure for genomics

Gcp For Bioinformatics ⭐ 178

GCP for Bioinformatics Researchers

Pathomicfusion ⭐ 148

Fusing Histology and Genomics via Deep Learning - IEEE TMI

Deep Learning Genomics Primer ⭐ 137

Contains files for the deep learning in genomics primer.

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them

Mapping out the coarse-grained connectivity structures of complex manifolds.

Genomicsnotebook ⭐ 84

Jupyter Notebooks on Azure for Genomics Data Analysis

Porpoise ⭐ 83

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

Extensible specification for representing and uniquely identifying biological sequence variation

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

Interactive assembly and analysis of RAD-seq data sets

Genomics In The Cloud ⭐ 63

Source code and related materials for the O'Reilly book

Histosketching Using Little Kmers

xHLA: Fast and accurate HLA typing from short read sequence data

Genomic_benchmarks ⭐ 52

Benchmarks for classification of genomic sequences

Full_spectrum_bioinformatics ⭐ 47

An open-access bioinformatics text

Elucidating the Utility of Genomic Elements with Neural Nets

Vrs Python ⭐ 44

GA4GH Variation Representation Python Implementation

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

Biopython Coronavirus ⭐ 39

Biopython Jupyter Notebook tutorial to characterize a small genome

Aws For Bioinformatics ⭐ 38

AWS for Bioinformatics Researchers

Pathogen Informatics Training ⭐ 38

GFA insert into GenomicSQLite

Genome Sketching ⭐ 33

online notebooks for a review of genome sketching

Chromdragonn ⭐ 29

Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"

Stratipy ⭐ 29

Graph regularized nonnegative matrix factorization (GNMF) in Python

Mmtf Genomics ⭐ 25

Methods for mapping genomic data onto 3D protein structure.

Concise: Keras extension for regulatory genomics

Gdsctools ⭐ 23

Tools related to the Genomics of Drug Sensitivity in Cancer (GDSC) projects (http://www.cancerrxgene.org/ )

Sequencework ⭐ 22

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Datalab Examples ⭐ 22

Example Cloud Datalab iPython Notebooks for genomics use cases.

Mosaicatcher Pipeline ⭐ 19

Integrated workflow for SV calling from single-cell Strand-seq data

Synthetic Data Genomics ⭐ 17

Proof of concept code from Gretel.ai and Illumina using generative neural networks to create synthetic versions of mouse genotype and phenotype data.

Cmm262 2020 ⭐ 16

Quantitative Methods in Genetics and Genomics Course 2020

Recipes and Tutorials for Automation & Extension on the CGC and SBPLAT platforms

Omxware Getting Started ⭐ 15

Examples to get started with IBM Functional Genomics Platform

In-silico Saturation Mutagenesis implementation with 10x or more speedup for certain architectures.

Visium Clustergrammer2 ⭐ 14

Spatial Transcriptomics Dashboard

A fast tool for detecting and decomposing segmental duplications in genome assemblies

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

Tiledb Examples ⭐ 13

Notebooks which are dedicated examples for TileDB

Crispulator.jl ⭐ 12

✂️ Pooled CRISPR screen optimization tool

Python Genomics ⭐ 12

A set of files to do genomics analysis on python

Genomic Biodiversity Interest Group

Secimtools ⭐ 10

A set of metabolomics tools for use in Galaxy

Microbial_amr_ml ⭐ 10

Code repository for machine learning and computational analysis of large-scale microbial genomics data (https://rdcu.be/9rHj)

Cgat Flow ⭐ 10

cgat-flow repository

Jp_gene_viz ⭐ 10

A collection of visualizations for genomics related information for use with Jupyter notebooks.

Genomics ⭐ 10

Deep learning in genomics

Python Library for data analysis based on GMQL

Nlp Approach For Prediction Of Gene Function With Dna Sequencing ⭐ 9

Fourier_attribution_priors ⭐ 8

An attribution prior for deep learning based on Fourier transforms

Haplotype phaser for next-generation sequencing data

Pathogenie ⭐ 7

Desktop tool for microbial genome annotation and gene detection

Single Cell Experiments ⭐ 7

Experiments to run single cell analyses efficiently at scale using Zarr, anndata, Scanpy, and Apache Spark

Code, data and analysis for moslin.

D N N_health Care ⭐ 7

Phage Host Prediction ⭐ 7

Published in PLOS ONE. We show that using embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features for phage-host interaction prediction — with the highest performance obtained using the transformer-based protein language model ProtT5

Plotly Demo ⭐ 7

Genomics with Plot.ly demonstration materials

Snipgenie ⭐ 6

command line and desktop tool for microbial variant calling

NvTK (NvwaToolKit), is a systemmatic and easy-using deep learning software in single-cell genomics.

Cite Sort ⭐ 6

Blast Binder ⭐ 6

Repo for running command line-based BLAST in Jupyter environment provided via Binder.

Teaching Comp Genomics Vis ⭐ 6

Comparative Genomics and Visualisation teaching module

Python Outbreak Info ⭐ 5

Python package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info

DBFE is a Python library with feature extraction methods that facilitate classifier learning from distributions of genomic variants.

Tensorflow_tutorial_genomics ⭐ 5

A collection of TensorFlow tutorials to analyze genomics datasets

Populationgenomicscourse ⭐ 5

Course in population genomics at BiRC

ProkEvo - an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.

Teaching Embl Plant Path Genomics ⭐ 5

Presentation and example material for the EMBL Plant and Pathogen Genomics workshop, 8-11 July 2014

Patric_tools ⭐ 5

Python package to interact with the PATRIC database (https://www.patricbrc.org)

Appliedgenomics2020 ⭐ 5

Description Materials for Spring 2020 Applied Genomics Course

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