Topic 176

researchers user interface software open easy source automated graphical tools learning bioinformatics deep programming datasets available users training raw tool algorithms databases ai access data intuitive platform friendly applications computer https analysis format convolutional present classification pipeline machine command image clinicians use formats created hardware public based environments virus allows facilitate train file cloud consuming research free images real infrastructure enable able trained database next implementation sharing biomedical refseq performance sophisticated task integration generation expertise standard frames covid will automatically web neural pipelines sequences viruses developed become integrates coronavirus search computing annotation provides tracking time 19 skills virtual metagenomic 2019

34 items. Top items listed below.

SIMON: open-source knowledge discovery platform 176 62 4

ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data 176 62 4

DeepEthogram: a machine learning pipeline for supervised behavior classification from raw pixels 176 26 13 4 2

AIDeveloper: deep learning image classification in life science and beyond 176 26 4

DamageProfiler: Fast damage pattern calculation for ancient DNA 176 62 4

EPySeg: a coding-free solution for automated segmentation of epithelia using deep learning 176 62 4

U-Infuse: Democratization of Customizable AI for Object Detection 176 62 26 4

Accurate And Versatile 3D Segmentation Of Plant Tissues At Cellular Resolution 176 70 26 18 4

Rtrack: a software package for reproducible automated water maze analysis 176 62 30 26 4

Interpretable detection of novel human viruses from genome sequencing data 176 26 4 1

Multi-Object Tracking in Heterogeneous environments (MOTHe) for animal video recordings 176 13 4 2

IDseq - An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring 176 125 62 4

SLEAP: Multi-animal pose tracking 176 26 4 2

Ethoflow: computer vision and artificial intelligence-based software for automatic behavior analysis 176 26 4 2

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response 176 62 1

COVIDier: A Deep-learning Tool For Coronaviruses Genome And Virulence Proteins Classification 176 37 26 1

The MRC IEU OpenGWAS data infrastructure 176 62 19 13 4

MetaGenomic analysis of short and long reads 176 62 25 4

Short k-mer Abundance Profiles Yield Robust Machine Learning Features and Accurate Classifiers for RNA Viruses 176 26 4

Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes 176 37 13 1

FlyBrainLab: Accelerating the Discovery of the Functional Logic of the Fruit Fly Brain in the Connectomic/Synaptomic Era 176 62 4 2

VirusDIP: Virus Data Integration Platform 176 37 1

BonVision - an open-source software to create and control visual environments 176 62 59 2

DIVA: natural navigation inside 3D images usingvirtual reality 176 62 13 4

No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics 176 13 1

Automated prediction and annotation of small proteins in microbial genomes 176 26 4

Databiology Lab CORONAHACK: Collection of Public COVID-19 Data 176 37 1

Cenote-Taker 2 Democratizes Virus Discovery and Sequence Annotation 176 165 62 4

TRex, a fast multi-animal tracking system with markerless identification, 2D body posture estimation and visual field reconstruction 62 30 4

deepMINE - Natural Language Processing based Automatic Literature Mining and Research Summarization for Early Stage Comprehension in Pandemic Situations specifically for COVID-19 176 37 4 1

HistoFlow: Label-Efficient and Interactive Deep Learning Cell Analysis 26 4

Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank 176 13 4

CUBIC-Cloud: An Integrative Computational Framework Towards Community-Driven Whole-Mouse-Brain Mapping 176 62 18 4

DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation 62 26 4

TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data 62 13 4

GIANI: open-source software for automated analysis of 3D microscopy images 62 13 4

ExoNet Database: Wearable Camera Images of Human Locomotion Environments 176 4

Bi-channel Image Registration and Deep-learning Segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain 62 26 4 2

The Mouse Action Recognition System (MARS): a software pipeline for automated analysis of social behaviors in mice 195 62 59 4 2

SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities 165 62 13 7 4

NeuroPycon: An open-source Python toolbox for fast multi-modal and reproducible brain connectivity pipelines 62 13 4

Giotto, a toolbox for integrative analysis and visualization of spatial expression data 62 43 4

Dix-seq: An integrated pipeline for fast amplicon data analysis 13 4

BingleSeq: A user-friendly R package for Bulk and Single-cell RNA-Seq Data Analysis 62 43 4

animalcules: Interactive Microbiome Analytics 1 and Visualization in R 13 4

mbkmeans: fast clustering for single cell data using mini-batch k-means 147 43 13 4

Neuroscience Cloud Analysis As a Service 62 4

Bactopia: a flexible pipeline for complete analysis of bacterial genomes 13 4

PanGIA: A Metagenomics Analytical Framework for RoutineBiosurveillance and Clinical Pathogen Detection 13 4

Simple Behavioral Analysis (SimBA): an open source toolkit for computer classification of complex social behaviors in experimental animals 62 26 4 2

TBtools - an integrative toolkit developed for interactive analyses of big biological data 165 62 13 4

EZcalcium: Open Source Toolbox for Analysis of Calcium Imaging Data 62 59 4 2

Detection of pre-microRNA with Convolutional Neural Networks 105 26 4

HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data 62 4 2

Multi Locus View: An Extensible Web Based Tool for the Analysis of Genomic Data 13 4

Metabolic pathway inference using multi-label classification with rich pathway features 26 4

Corna - An Open Source Python Tool For Natural Abundance Correction In Isotope Tracer Experiments 62 13 4

mzMLb: a future-proof raw mass spectrometry data format based on standards-compliant mzML and optimized for speed and storage requirements 176 45 4

CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations 62 13 4

Kaleidoscope: A New Bioinformatics Pipeline Web Application for In Silico Hypothesis Exploration of Omics Signatures 62 13 4

OpSeF: Open source Python framework for collaborative instance segmentation of bioimages 62 26 4

The Gene Expression Deconvolution Interactive Tool (GEDIT): Accurate Cell Type Quantification from Gene Expression Data 13 4

The UCSC SARS-CoV-2 Genome Browser 37 1

Alignment-free machine learning approaches for the lethality prediction of potential novel human-adapted coronavirus using genomic nucleotide 37 26 1

PAWER: Protein Array Web ExploreR 62 13 4

Automated cell tracking using StarDist and TrackMate 62 18 4

Automated Isoform Diversity Detector (AIDD): A pipeline for investigating transcriptome diversity of RNA-seq data 62 4

InstantDL - An easy-to-use deep learning pipeline for image segmentation and classification 13 4

PartSeg, a Tool for Quantitative Feature Extraction From 3D Microscopy Images for Dummies 62 4

MazeMaster: an open-source Python-based software package for controlling virtual reality experiments 62 59 4 2

Functional assessments of PTEN variants using machine-assisted phenotype scoring 26 4

Making data-driven hypotheses for gene functions by integrating dependency, expression, and literature data 62 4

DCP: a pipeline toolbox for diffusion connectome 62 59 13 4 2

DeepCINAC: a deep-learning-based Python toolbox for inferring calcium imaging neuronal activity based on movie visualization 26 4 2

ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses 62 4

An automated framework for efficiently designing deep convolutional neural networks in genomics 26 4

SARS-CoV-2 sequence typing, evolution and signatures of selection using CoVa, a Python-based command-line utility 37 1

SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat 165 62 13 4

Graphia: A platform for the graph-based visualisation and analysis of complex data 62 13 4

Haplotracker: a web application for simple and accurate mitochondrial haplogrouping using short DNA fragments 145 4

anTraX: high throughput video tracking of color-tagged insects 62 4

NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization 62 13 4

NanoReviser: An Error-correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm 13 4

SMAP - A Modular Superresolution Microscopy Analysis Platform for SMLM Data 62 4

MiBiOmics: An interactive web application for multi-omics data exploration and integration 62 13 4

PhenoImage: an open-source GUI for plant image analysis 62 4

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data 13 4

Interpreting blood GLUcose data with R package iglu 62 13 4

Probabilistic Harmonization and Annotation of Single-cell Transcriptomics Data with Deep Generative Models 43 4

ORACA: an open source software for Online Realtime neural Activity extraction and offline Cross session Analysis 62 59 4 2

Streamlining Data-Intensive Biology With Workflow Systems 62 4

Sleep Identification Enabled by Supervised Training Algorithms (SIESTA): An open-source platform for automatic sleep staging of rodent polysomnographic data 26 4

BioDynaMo: an agent-based simulation platform for scalable computational biology research 62 4

Real-time resolution of short-read assembly graph using ONT long reads 13 4

Location Invariant Animal Recognition UsingMixed Source Datasets and Deep Learning 131 26 4

CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning 162 13 4

ATAV: a comprehensive platform for population-scale genomic analyses 165 62 13 4

Identifying Genomic Islands with Deep Neural Networks 26 4

Meta-Signer: Metagenomic Signature Identifier based on Rank Aggregation of Features 26 4

GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline 13 4