PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
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OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies
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Deep Learning tools for brain medical images
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Calculation of interatomic interactions in molecular structures
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FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.
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Useful library for validation of Bitcoin, Litecoin, Ethereum and other cryptocoin addresses
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Tool to visualize gigantic pathology images and use AI to segment cancer cells and present as an overlay
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Sim racing result reader for PHP
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Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
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Data Wrangling and Processing for Genomics
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Protein sequence classification with self-supervised pretraining
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NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
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An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies
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PyTorch implementation of 'Squeeze and Excite' Guided Few Shot Segmentation of Volumetric Scans
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ECP-CANDLE Benchmarks
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PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
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medical-transcription-analysisby aws-samples
JavaScript 
52 Version:Current License: Proprietary (Proprietary)
Medical Transcription Analysis (MTA) demonstrates how the integration of Amazon Comprehend Medical and Amazon Transcribe Medical can be used to transcribe audio data, extract key medical components and tag the data to their corresponding entities. Automating the medical transcription and comprehension process makes it easier for health care professionals to focus on patient care.
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NHSX and the British Society of Thoracic Imaging (BSTI) have formed a joint partnership in order to create a national database of chest X-ray and CT images. This is to enable the validation and development of automated analysis technologies, and to promote research projects in response to the COVID-19 pandemic.
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The open source toolbox for reproducible diffusion MRI-based microstructure estimation
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A collection of deep learning models with a unified API.
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Code for design of diagnostic PCR primers, and metabarcoding markers.
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Code for phasing SVs with SNPs
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API for linked biological knowledge
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Python package to annotate and visualize gene fusions.
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A pipeline and a framework for NGS analysis (RNA-Seq and soon Chip-Seq)
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Simple pure Python SAM parser and objects for working with SAM records
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covid19-greece-apiby Covid-19-Response-Greece
Python 46 Version:Current License: Strong Copyleft (EUPL-1.2)
🦠 A simple and fast API for tracking the coronavirus (COVID-19) outbreak in Greece 🇬🇷
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High throughput protein function annotation with Human Readable Description (HRDs) and Gene Ontology (GO) Terms.
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A command line tool in python to fetch worldwide data about COVID-19
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de novo virus assembler of Illumina paired reads
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Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
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PartitionFinder discovers optimal partitioning schemes for DNA sequences.
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Rapid analysis and visualization of coronavirus genome variation
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Coronavirus COVID19 US Cases Dashboard
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Discord Bot for info on novel coronavirus (COVID-19)
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Simulate a pandemic with artificial life objects.
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A tool for fast and accurate summarizing of variant calling format (VCF) files
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Corresponding code of 'Quiros A.C., Murray-Smith R., Yuan K. Pathology GAN: Learning deep representations of cancer tissue. Proceedings of The 3rd International Conference on Medical Imaging with Deep Learning (MIDL) 2020'
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An evolutionary computation framework
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ARCHS4 RNA-seq processing scripts and web server pages.
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The depository support training and testing BERT-CNN model on three medical relation extraction corpora: BioCreative V CDR task corpus, traditional Chinese medicine literature corpus, and i2b2 temporal relation corpus.
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Tutorials, workflows, and convenience scripts for Single Cell Portal
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Python package to fetch information regarding the novel corona virus provided by Johns Hopkins university and worldometers.info
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CollaboNet for Biomedical Named Entity Recognition
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Modelling the Language of Life - Deep Learning Protein Sequences
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GeneMANIA helps you predict the function of your favourite genes and gene sets.
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Learn interpretable computational phenotyping models from k-merized genomic data
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DeepEventMine: End-to-end Neural Nested Event Extraction from Biomedical Texts
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Skin_Lesion_Detection_Deep_Learningby adriaromero
Python 39 Version:Current
License: No License (No License)
License: No License (No License)Skin lesion detection from dermoscopic images using Convolutional Neural Networks
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pymodby pymodproject
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
Python 59Updated: 1 y ago License: Weak Copyleft (LGPL-2.1)
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OMOP2OBOby callahantiff
OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies
Jupyter Notebook 58Updated: 1 y ago License: Permissive (MIT)
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deepbrainby iitzco
Deep Learning tools for brain medical images
Python 57Updated: 3 y ago License: Permissive (MIT)
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arpeggioby harryjubb
Calculation of interatomic interactions in molecular structures
Python 56Updated: 1 y ago License: Strong Copyleft (GPL-3.0)
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FluentDNAby josiahseaman
FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.
JavaScript 56Updated: 1 y ago License: No License (No License)
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crypto-address-validatorby Swyftx
Useful library for validation of Bitcoin, Litecoin, Ethereum and other cryptocoin addresses
JavaScript 54Updated: 2 y ago License: Permissive (MIT)
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DigiPathAIby haranrk
Tool to visualize gigantic pathology images and use AI to segment cancer cells and present as an overlay
JavaScript 54Updated: 1 y ago License: Permissive (MIT)
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simresultsby mauserrifle
Sim racing result reader for PHP
PHP 54Updated: 11 mo ago License: Permissive (ISC)
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TranscriptCleanby mortazavilab
Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome
Python 53Updated: 12 mo ago License: Permissive (MIT)
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wrangling-genomicsby datacarpentry
Data Wrangling and Processing for Genomics
Shell 53Updated: 11 mo ago License: Proprietary (Proprietary)
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UDSMProtby nstrodt
Protein sequence classification with self-supervised pretraining
Python 53Updated: 3 y ago License: Proprietary (Proprietary)
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NeoDTIby FangpingWan
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
Python 53Updated: 3 y ago License: Permissive (Apache-2.0)
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OSGenomeby mentatpsi
An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies
Python 53Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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few-shot-segmentationby abhi4ssj
PyTorch implementation of 'Squeeze and Excite' Guided Few Shot Segmentation of Volumetric Scans
Python 52Updated: 3 y ago License: Permissive (MIT)
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pathway-mapperby iVis-at-Bilkent
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
TypeScript 52Updated: 1 y ago License: Strong Copyleft (AGPL-3.0)
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medical-transcription-analysisby aws-samples
Medical Transcription Analysis (MTA) demonstrates how the integration of Amazon Comprehend Medical and Amazon Transcribe Medical can be used to transcribe audio data, extract key medical components and tag the data to their corresponding entities. Automating the medical transcription and comprehension process makes it easier for health care professionals to focus on patient care.
JavaScript 52Updated: 2 y ago License: Proprietary (Proprietary)
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covid-chest-imaging-databaseby nhsx
NHSX and the British Society of Thoracic Imaging (BSTI) have formed a joint partnership in order to create a national database of chest X-ray and CT images. This is to enable the validation and development of automated analysis technologies, and to promote research projects in response to the COVID-19 pandemic.
Python 51Updated: 1 y ago License: Permissive (MIT)
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dmipyby AthenaEPI
The open source toolbox for reproducible diffusion MRI-based microstructure estimation
Python 50Updated: 3 y ago License: Permissive (MIT)
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modelhubby modelhub-ai
A collection of deep learning models with a unified API.
Python 50Updated: 3 y ago License: Permissive (MIT)
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find_differential_primersby widdowquinn
Code for design of diagnostic PCR primers, and metabarcoding markers.
Python 50Updated: 11 mo ago License: Permissive (MIT)
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crossstitchby schatzlab
Code for phasing SVs with SNPs
Java 49Updated: 1 y ago License: No License (No License)
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biolink-apiby biolink
API for linked biological knowledge
Python 49Updated: 2 y ago License: Permissive (BSD-3-Clause)
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AGFusionby murphycj
Python package to annotate and visualize gene fusions.
Python 47Updated: 1 y ago License: Permissive (MIT)
47Updated: 1 y ago License: Permissive (MIT)Support
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eoulsanby GenomicParisCentre
A pipeline and a framework for NGS analysis (RNA-Seq and soon Chip-Seq)
Java 46Updated: 2 y ago License: Proprietary (Proprietary)
46Updated: 2 y ago License: Proprietary (Proprietary)Support
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simplesamby mdshw5
Simple pure Python SAM parser and objects for working with SAM records
Python 46Updated: 3 y ago License: Permissive (MIT)
46Updated: 3 y ago License: Permissive (MIT)Support
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covid19-greece-apiby Covid-19-Response-Greece
🦠 A simple and fast API for tracking the coronavirus (COVID-19) outbreak in Greece 🇬🇷
Python 46Updated: 1 y ago License: Strong Copyleft (EUPL-1.2)
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AHRDby groupschoof
High throughput protein function annotation with Human Readable Description (HRDs) and Gene Ontology (GO) Terms.
Java 46Updated: 3 y ago License: Proprietary (Proprietary)
46Updated: 3 y ago License: Proprietary (Proprietary)Support
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Explorable-Super-Resolutionby YuvalBahat
Python 45Updated: 3 y ago License: Permissive (Apache-2.0)
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coronapy-cliby MouadBH
A command line tool in python to fetch worldwide data about COVID-19
Python 44Updated: 3 y ago License: Permissive (MIT)
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ivaby sanger-pathogens
de novo virus assembler of Illumina paired reads
Python 44Updated: 1 y ago License: Proprietary (Proprietary)
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2020plusby KarchinLab
Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
Python 43Updated: 3 y ago License: Permissive (Apache-2.0)
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partitionfinderby brettc
PartitionFinder discovers optimal partitioning schemes for DNA sequences.
Python 43Updated: 3 y ago License: Proprietary (Proprietary)
43Updated: 3 y ago License: Proprietary (Proprietary)Support
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covizuby PoonLab
Rapid analysis and visualization of coronavirus genome variation
JavaScript 43Updated: 11 mo ago License: Permissive (MIT)
43Updated: 11 mo ago License: Permissive (MIT)Support
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front-endby ncov19-us
Coronavirus COVID19 US Cases Dashboard
Python 42Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
42Updated: 3 y ago License: Strong Copyleft (GPL-3.0)Support
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coronavirus-botby picklejason
Discord Bot for info on novel coronavirus (COVID-19)
Python 42Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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Pandemic-Simulatorby IvanHornung
Simulate a pandemic with artificial life objects.
Java 41Updated: 3 y ago License: Permissive (Apache-2.0)
41Updated: 3 y ago License: Permissive (Apache-2.0)Support
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cerebraby czbiohub
A tool for fast and accurate summarizing of variant calling format (VCF) files
Python 41Updated: 3 y ago License: Permissive (MIT)
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Pathology-GANby AdalbertoCq
Corresponding code of 'Quiros A.C., Murray-Smith R., Yuan K. Pathology GAN: Learning deep representations of cancer tissue. Proceedings of The 3rd International Conference on Medical Imaging with Deep Learning (MIDL) 2020'
Python 41Updated: 3 y ago License: No License (No License)
41Updated: 3 y ago License: No License (No License)Support
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evolvableby mattruzicka
An evolutionary computation framework
Ruby 41Updated: 2 y ago License: Permissive (MIT)
41Updated: 2 y ago License: Permissive (MIT)Support
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archs4by MaayanLab
ARCHS4 RNA-seq processing scripts and web server pages.
JavaScript 41Updated: 3 y ago License: Proprietary (Proprietary)
41Updated: 3 y ago License: Proprietary (Proprietary)Support
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MedicalRelationExtractionby chentao1999
The depository support training and testing BERT-CNN model on three medical relation extraction corpora: BioCreative V CDR task corpus, traditional Chinese medicine literature corpus, and i2b2 temporal relation corpus.
Python 41Updated: 3 y ago License: Permissive (MIT)
41Updated: 3 y ago License: Permissive (MIT)Support
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single_cell_portalby broadinstitute
Tutorials, workflows, and convenience scripts for Single Cell Portal
Python 40Updated: 3 y ago License: Permissive (BSD-3-Clause)
40Updated: 3 y ago License: Permissive (BSD-3-Clause)Support
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covidby ahmednafies
Python package to fetch information regarding the novel corona virus provided by Johns Hopkins university and worldometers.info
Python 40Updated: 3 y ago License: Permissive (MIT)
40Updated: 3 y ago License: Permissive (MIT)Support
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CollaboNetby wonjininfo
CollaboNet for Biomedical Named Entity Recognition
Python 40Updated: 3 y ago License: Proprietary (Proprietary)
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SeqVecby mheinzinger
Modelling the Language of Life - Deep Learning Protein Sequences
Python 40Updated: 3 y ago License: Permissive (MIT)
40Updated: 3 y ago License: Permissive (MIT)Support
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genemaniaby GeneMANIA
GeneMANIA helps you predict the function of your favourite genes and gene sets.
Java 39Updated: 11 mo ago License: No License (No License)
39Updated: 11 mo ago License: No License (No License)Support
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koverby aldro61
Learn interpretable computational phenotyping models from k-merized genomic data
Python 39Updated: 3 y ago License: Strong Copyleft (GPL-3.0)
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DeepEventMineby aistairc
DeepEventMine: End-to-end Neural Nested Event Extraction from Biomedical Texts
Python 39Updated: 3 y ago License: Permissive (Apache-2.0)
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Skin_Lesion_Detection_Deep_Learningby adriaromero
Skin lesion detection from dermoscopic images using Convolutional Neural Networks
Python 39Updated: 3 y ago License: No License (No License)
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