Topic 62

user software bioinformatics users tools package friendly open interface web tool available source interactive data datasets easy python visualization platform graphical https researchers analysis provides freely developed accessible automated workflows reproducible research allows present use easily computational org intuitive database pipeline programming community packages http facilitate implementation application based visualisation comprehensive workflow access large www designed biological enables biomedical framework providing processing resource image applications scientific can computing scientists existing quality will resources introduce online cloud integrates analyses raw visualize format exploration throughput integrated any pipelines perform an it biologists command algorithms automatically files new scale run flexible expertise code

317 items. Top items listed below.

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

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

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

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

SIMON: open-source knowledge discovery platform 176 62 4

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

PAWER: Protein Array Web ExploreR 62 13 4

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

ideal: an R/Bioconductor package for Interactive Differential Expression Analysis 62 13 4

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

Comparison of visualisation tools for single-cell RNAseq data 62 13 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

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

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

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

CHOmics: a web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines 62 13 4

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

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

PYMEVisualize: an open-source tool for exploring 3D super-resolution data 62 18 4

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

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

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

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics 62 38 4

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

ProTrack: An Interactive Multi-Omics Data Browser for Proteogenomic Studies 62 13 4

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

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

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

Streamlining Data-Intensive Biology With Workflow Systems 62 4

pyTFM: A tool for Traction Force and Monolayer Stress Microscopy 62 13 4

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

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

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

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

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

BIAFLOWS: A collaborative framework to reproducibly deploy and benchmark bioimage analysis workflows 62 4

RAVE: comprehensive open-source software for reproducible analysis and visualization of intracranial EEG data 62 59 4 2

GCA: An R package for genetic connectedness analysis using pedigree and genomic data 62 13 4

Rcirc: an R package for circRNA analyses and visualization 13 4

Interpreting blood GLUcose data with R package iglu 62 13 4

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

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

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

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

Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation 62 4

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

DrawAlignR: An interactive tool for across run chromatogram alignment visualization 13 4

i2dash: Creation of Flexible, Interactive and Web-based Dashboards for Visualization of Omics-pipeline Results 184 62 7 4

The Atlas of Inflammation-Resolution (AIR) 62 4

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

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

TimeTrial: An Interactive Application for Optimizing the Design and Analysis of Transcriptomic Times-Series Data in CircadianBiology Research 62 4

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

Automated cell tracking using StarDist and TrackMate 62 18 4

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

LongGeneDB: a data hub for long genes 62 13 9 4

Shiny-SoSV: A web-based performance calculator for somatic structural variant detection 62 13 4

SambaR: an R package for fast, easy and reproducible population-genetic analyses of biallelic SNP datasets 62 13 4

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

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

Neuroscience Cloud Analysis As a Service 62 4

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

OPENANNO: annotating genomic regions with chromatin accessibility 62 4

PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments 169 7 4

ProNetView-ccRCC: A web-based portal to interactively explore clear cell renal cell carcinoma proteogenomics networks 62 4

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

RAD: a web application to identify region associated differentially expressed genes 165 62 31 13 4

Computational Tool for Ensemble Averaging of Single-Molecule Data 62 18 4

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

Brain Modeling ToolKit: an Open Source Software Suite for Multiscale Modeling of Brain Circuits 62 4

NoRCE: Non-coding RNA Sets Cis Enrichment Tool 13 4

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

DUBS: A Framework for Developing Directory of Useful Benchmarking Sets for Virtual Screening 62 4

modleR: a modular workflow to perform ecological niche modeling in R 62 4

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

ORCESTRA: a platform for orchestrating and sharing high-throughput pharmacogenomic analyses 62 4

Comparison of High-Throughput Single-Cell RNA Sequencing Data Processing Pipelines 43 4

mrMLM v4.0: An R Platform for Multi-locus Genome-wide Association Studies 62 13 4

piRPheno: a manually curated database to prioritize and analyze human disease related piRNAs 165 62 13 4

SEPIA - SuscEptibility mapping PIpeline tool for phAse images 62 59 4

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

TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment 43 9 4

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

How to use online tools to generate new hypotheses for mammary gland biology research: a case study for Wnt7b 62 4

MetaFunc: Taxonomic and Functional Analyses of High Throughput Sequencing for Microbiomes 13 4

Pancreatlas: applying an adaptable framework to map the human pancreas in health and disease 62 13 4

User-friendly, scalable tools and workflows for single-cell analysis 62 43 13 4

scTPA: A web tool for single-cell transcriptome analysis of pathway activation signatures 43 4

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

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

CorRelator: An interactive and flexible toolkit for high-precision cryo-correlative light and electron microscopy 62 13 4

Bio-Node - Bioinformatics in the Cloud 62 13 4

Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data for Chinese Glioma Patients 62 9 4

KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species 62 4

An adaptable analysis workflow for characterization of platelet spreading and morphology 62 4

EMU: reconfigurable graphical user interfaces for Micro-Manager 62 4

miEAA 2.0: Integrating multi-species microRNA enrichment analysis and workflow management systems 62 13 4

scLM: automatic detection of consensus gene clusters across multiple single-cell datasets 147 43 13 4

pMAT: An Open-Source Software Suite for the Analysis of Fiber Photometry Calcium Imaging 62 59 18 4

What does your cell really do? Model-based assessment of mammalian cells metabolic functionalities using omics data 62 43 4