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71 search results found

Bottom Up Attention ⭐ 979

Bottom-up attention model for image captioning and VQA, based on Faster R-CNN and Visual Genome

Visual_genome_python_driver ⭐ 328

A python wrapper for the Visual Genome API

Ideogram ⭐ 265

Chromosome visualization for the web

Datasets ⭐ 259

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

Convolutional neural network analysis for predicting DNA sequence activity.

Gena_lm ⭐ 120

GENA-LM is a transformer masked language model trained on human DNA sequence.

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

Peregrine ⭐ 94

Peregrine: Fast Genome Assembler Using SHIMMER Index

Tabula Muris Senis ⭐ 81

Tabula Muris Senis

Hic Data Analysis Bootcamp ⭐ 78

Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.

Neoantigen Vaccine Pipeline ⭐ 72

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines

Variant Qc ⭐ 61

Quality control methods for human genomic variants.

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph

Space Time ⭐ 45

Analysis of EBOV genome sequence from Guinea, Sierra Leone and Liberia from 2014-2016

Metage2metabo ⭐ 42

From annotated genomes to metabolic screening in large scale microbiotas

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

Ley Lab MetaGenome Profiler DataBase generator

Biopython Coronavirus ⭐ 39

Biopython Jupyter Notebook tutorial to characterize a small genome

Genome Grist ⭐ 34

map Illumina metagenomes to genomes!

Bottom Up Attention Ai Challenger ⭐ 33

Genome Sketching ⭐ 33

online notebooks for a review of genome sketching

Bacterial Annotation by Learned Representation of Genes

The code and output of our AAAI paper "Knowledge-Enriched Visual Storytelling"

3d Genome Processing Tutorial ⭐ 28

A 3D genome data processing tutorial for ISMB/ECCB 2017

Vg_cleansing ⭐ 24

dataset cleansing for Visual Genome

Grupo Estudo Bioinformatica ⭐ 22

Repositório do grupo de estudo de Bioinformática da rede de comunidades das PyLadies Brasil.

Datalab Examples ⭐ 22

Example Cloud Datalab iPython Notebooks for genomics use cases.

Pyparanoid ⭐ 22

Rapid and scalable homolog identification for bacterial genomes

Crisprdisco ⭐ 21

CRISPR discovery pipeline

Jbrowse Jupyter ⭐ 21

A python package for showing JBrowse views

Rambutan ⭐ 20

Prediction of the 3D structure of the genome through statistically significant Hi-C contacts.

Genomedisco ⭐ 18

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

Crispriadesign ⭐ 17

Reference Phylogeny for Bacterial and Archaeal Genomes

Refseq_masher ⭐ 15

Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database

Coronavirus Knowledge Graph ⭐ 14

OBSOLETE: Prototype Neo4j Knowledge Graph for Coronavirus outbreaks (new version: https://github.com/sbl-sdsc/coronavirus-knowledge-

Phrasecutdataset ⭐ 14

Dataset API for "PhraseCut: Language-based Image Segmentation in the Wild"

Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data

Prophagepredictioncomparisons ⭐ 14

Comparisons of multiple different prophage predictions

Nanotext ⭐ 13

Proteins as words, genomes as documents.

Deepmased ⭐ 13

Deep learning for Metagenome Assembly Error Detection

Alleleanalyzer ⭐ 13

A software tool for personalized and allele-specific CRISPR editing.

Te Search Tools ⭐ 11

Python wrappers for programs that search for transposable elements

Calling deletions using deep convolutional neural

Teaching materials for SymbNET course: from MAGs to GEMs

Mackinac ⭐ 10

Mackinac: A bridge between ModelSEED and COBRApy

Plasmidminer ⭐ 10

🔍 in silico plasmid extraction

Python Genome Browser ⭐ 9

Tools for making plots of genomic datasets in a genome-browser-like format

Pancancer Evaluation ⭐ 9

Evaluating genome-wide prediction of driver mutations using pan-cancer data

Emapper Benchmark ⭐ 9

Raw data and scripts used to benchmark eggnog-mapper. Analysis and additional tests cases are provided as a python notebook.

Engineering ⭐ 8

Engineering website

Temporal Features For Nonres Buildings Library ⭐ 8

Jupyter notebooks for the Energy and Buildings Publication

Graph_summarization ⭐ 8

Browser for Graph Genomes built with VG based on Graph Summarization to provide semantic zoom. As a user zooms in on a graph genome, the topology becomes more complex. Provides visualization for variation within a species of plant or animal. Designed to scale up to thousands of specimens and provide useful visualizations.

Perchlorate Metagenome 2018 ⭐ 8

Scripts used in the publication Tyler P. Barnum, Israel A. Figueroa, Charlotte I. Carlström, Lauren N. Lucas, Anna L. Engelbrektson, and John D. Coates. (2018) Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities.

Deep_learning_genomics_nlp ⭐ 7

Final project for CS224d

Pathogenie ⭐ 7

Desktop tool for microbial genome annotation and gene detection

Gnomad_mnv ⭐ 7

Multi-nucleotide variants (MNVs) in gnomAD 2.1

Gwas Lecture ⭐ 7

Lectures on Genome Wide Association Studies (GWAS) using Python, Limix and Jupyter Noteboos

Teaching Comp Genomics Vis ⭐ 6

Comparative Genomics and Visualisation teaching module

some code for linlog model simulation

Deepredmt ⭐ 6

Deepred-Mt is a novel method based on deep neural networks to predict C-to-U editing sites in angiosperm mitochondrial RNA.

R package for the identification of core-fitness and common-essential genes from joint analyses of multiple genome-wide CRISPR-Cas9 screens

Ncbi_jupyter ⭐ 5

A variety of NCBI Computational Tools Distributed as Jupyter Notebooks

Mite Tracker ⭐ 5

MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes

Spoonfednanopore ⭐ 5

The world's simplest open-source nanopore alignment and assembly algorithm

Covid19_population_genomics ⭐ 5

Analysis of the population diversity of SARS-CoV-2 within and between individual patients

Appliedgenomics2020 ⭐ 5

Description Materials for Spring 2020 Applied Genomics Course

Kallisto Scatac ⭐ 5

A suite of computational tools used for molecular inversion probe design, data processing, and analysis.

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

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