scholarly journals EvoLaps: a web interface to visualize continuous phylogeographic reconstructions

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
François Chevenet ◽  
Denis Fargette ◽  
Stéphane Guindon ◽  
Anne-Laure Bañuls
Keyword(s):  
Graphical Representations ◽  
Graphical Methods ◽  
Web Interface ◽  
Link Type ◽  
User Friendly

Abstract Background Phylogeographic reconstructions serve as a basis to understand the spread and evolution of pathogens. Visualization of these reconstructions often lead to complex graphical representations which are difficult to interpret. Result We present EvoLaps, a user-friendly web interface to visualize phylogeographic reconstructions based on the analysis of latitude/longitude coordinates with various clustering levels. EvoLaps also produces transition diagrams that provide concise and easy to interpret summaries of phylogeographic reconstructions. Conclusion The main contribution of EvoLaps is to assemble known numerical and graphical methods/tools into a user-friendly interface dedicated to the visualization and edition of evolutionary scenarios based on continuous phylogeographic reconstructions. EvoLaps is freely usable at www.evolaps.org.

scholarly journals A repository of web-based bioinformatics resources developed in India

2020 ◽  
Author(s):  
Abhishek Agarwal ◽  
Piyush Agrawal ◽  
Aditi Sharma ◽  
Vinod Kumar ◽  
Chirag Mugdal ◽  
...  
Keyword(s):  
Scientific Community ◽  
Biological Databases ◽  
Web Interface ◽  
Web Based ◽  
Link Type ◽  
Complete Detail ◽  
User Friendly

AbstractIndiaBioDb (https://webs.iiitd.edu.in/raghava/indiabiodb/) is a manually curated comprehensive repository of bioinformatics resources developed and maintained by Indian researchers. This repository maintains information about 543 freely accessible functional resources that include around 258 biological databases. Each entry provides a complete detail about a resource that includes the name of resources, web link, detail of publication, information about the corresponding author, name of institute, type of resource. A user-friendly searching module has been integrated, which allows users to search our repository on any field. In order to retrieve categorized information, we integrate the browsing facility in this repository. This database can be utilized for extracting the useful information regarding the present scenario of bioinformatics inclusive of all research labs funded by government and private bodies of India. In addition to web interface, we also developed mobile to facilitate the scientific community.

scholarly journals CancerVar: a web server for improved evidence-based clinical interpretation of cancer somatic mutations and copy number abnormalities

2020 ◽  
Author(s):  
Quan Li ◽  
Zilin Ren ◽  
Yunyun Zhou ◽  
Kai Wang
Keyword(s):  
Clinical Significance ◽  
Copy Number ◽  
Somatic Mutations ◽  
Relevant Information ◽  
Web Interface ◽  
Clinical Interpretation ◽  
Link Type ◽  
Command Line Tool ◽  
Hotspot Mutations ◽  
User Friendly

ABSTRACTSeveral knowledgebases, such as CIViC, CGI and OncoKB, have been manually curated to support clinical interpretations of somatic mutations and copy number abnormalities (CNAs) in cancer. However, these resources focus on known hotspot mutations, and discrepancies or even conflicting interpretations have been observed between these knowledgebases. To standardize clinical interpretation, AMP/ASCO/CAP/ACMG/CGC jointly published consensus guidelines for the interpretations of somatic mutations and CNAs in 2017 and 2019, respectively. Based on these guidelines, we developed a standardized, semi-automated interpretation tool called CancerVar (Cancer Variants interpretation), with a user-friendly web interface to assess the clinical impacts of somatic variants. Using a semi-supervised method, CancerVar interpret the clinical impacts of cancer variants as four tiers: strong clinical significance, potential clinical significance, unknown clinical significance, benign/likely benign. CancerVar also allows users to specify criteria or adjust scoring weights as a customized interpretation strategy, and allows phenotype-driven scoring for specific types of cancer. Importantly, CancerVar generates automated texts to summarize clinical evidence on somatic variants, which greatly reduces manual workload to write interpretations that include relevant information from harmonized knowledgebases. CancerVar can be accessed at http://cancervar.wglab.org and it is open to all users without login requirements. The command line tool is also available at https://github.com/WGLab/CancerVar.

scholarly journals MeltingPlot: a user-friendly online tool for epidemiological investigation using High Resolution Melting data

2020 ◽  
Author(s):  
Matteo Perini ◽  
Gherard Batisti Biffignandi ◽  
Domenico Di Carlo ◽  
Ajay Ratan Pasala ◽  
Aurora Piazza ◽  
...  
Keyword(s):  
High Resolution ◽  
High Resolution Melting ◽  
Epidemiological Studies ◽  
Supplementary Information ◽  
Web Interface ◽  
Web Tool ◽  
Online Tool ◽  
Link Type ◽  
Surveillance Programs ◽  
User Friendly

AbstractSummaryMeltingPlot is an open source web tool for pathogen typing and epidemiological investigations using High Resolution Melting (HRM) data. The tool implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. MeltingPlot also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological studies. HRM technique allows pathogen typing in less than 5 hours with ~5 euros per sample. MeltingPlot is the first tool specifically designed for HRM-based epidemiological studies and it can analyse hundreds of isolates in a few seconds. Thus, the use of MeltingPlot makes HRM-based typing suitable for large surveillance programs as well as for rapid outbreak reconstructions.Availability and implementationMeltingPlot is implemented in R.The web interface is available at https://skynet.unimi.it/index.php/tools/meltingplot.The source code is also available at https://github.com/MatteoPS/[email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals TCIApathfinder: an R client for The Cancer Imaging Archive REST API

2017 ◽  
Author(s):  
Pamela Russell ◽  
Kelly Fountain ◽  
Dulcy Wolverton ◽  
Debashis Ghosh
Keyword(s):  
Medical Images ◽  
Cancer Imaging ◽  
Web Interface ◽  
Large Database ◽  
Image Series ◽  
Link Type ◽  
Rest Api ◽  
User Friendly ◽  
R Functions

AbstractSummaryThe Cancer Imaging Archive (TCIA) hosts publicly available de-identified medical images of cancer from over 25 body sites and over 30, 000 patients. Over 400 published studies have utilized freely available TCIA images. Image series and metadata are available for download through a web interface or a REST API. We present TCIApathfinder, an R client for the TCIA REST API. TCIApathfinder wraps API access in user-friendly R functions that can be called within an R session or easily incorporated into scripts. Functions are provided to explore the contents of the large database and to download image files.Availability and implementationTCIApathfinder is available under the MIT license as a package on CRAN (https://cran.r-project.org/web/packages/TCIApathfinder/index.html) and at https://github.com/pamelarussell/[email protected]

scholarly journals Correlation AnalyzeR: functional predictions from gene co-expression correlations

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Henry E. Miller ◽  
Alexander J. R. Bishop
Keyword(s):  
Web Application ◽  
Bone Cancer ◽  
R Package ◽  
Limited Range ◽  
Web Interface ◽  
Generating Functional ◽  
Link Type ◽  
Genome Wide ◽  
User Friendly

Abstract Background Co-expression correlations provide the ability to predict gene functionality within specific biological contexts, such as different tissue and disease conditions. However, current gene co-expression databases generally do not consider biological context. In addition, these tools often implement a limited range of unsophisticated analysis approaches, diminishing their utility for exploring gene functionality and gene relationships. Furthermore, they typically do not provide the summary visualizations necessary to communicate these results, posing a significant barrier to their utilization by biologists without computational skills. Results We present Correlation AnalyzeR, a user-friendly web interface for exploring co-expression correlations and predicting gene functions, gene–gene relationships, and gene set topology. Correlation AnalyzeR provides flexible access to its database of tissue and disease-specific (cancer vs normal) genome-wide co-expression correlations, and it also implements a suite of sophisticated computational tools for generating functional predictions with user-friendly visualizations. In the usage example provided here, we explore the role of BRCA1-NRF2 interplay in the context of bone cancer, demonstrating how Correlation AnalyzeR can be effectively implemented to generate and support novel hypotheses. Conclusions Correlation AnalyzeR facilitates the exploration of poorly characterized genes and gene relationships to reveal novel biological insights. The database and all analysis methods can be accessed as a web application at https://gccri.bishop-lab.uthscsa.edu/correlation-analyzer/ and as a standalone R package at https://github.com/Bishop-Laboratory/correlationAnalyzeR.

scholarly journals webMCP-counter: a web interface for transcriptomics-based quantification of immune and stromal cells in heterogeneous human or murine samples

2020 ◽  
Author(s):  
Maxime Meylan ◽  
Etienne Becht ◽  
Catherine Sautès-Fridman ◽  
Aurélien de Reyniès ◽  
Wolf H. Fridman ◽  
...  
Keyword(s):  
Stromal Cells ◽  
R Package ◽  
Web Interface ◽  
Transcriptomic Data ◽  
R Programming Language ◽  
Link Type ◽  
Precise Estimation ◽  
R Packages ◽  
R Programming ◽  
User Friendly

AbstractSummaryWe previously reported MCP-counter and mMCP-counter, methods that allow precise estimation of the immune and stromal composition of human and murine samples from bulk transcriptomic data, but they were only distributed as R packages. Here, we report webMCP-counter, a user-friendly web interface to allow all users to use these methods, regardless of their proficiency in the R programming language.Availability and ImplementationFreely available from http://134.157.229.105:3838/webMCP/. Website developed with the R package shiny. Source code available from GitHub: https://github.com/FPetitprez/webMCP-counter.

Pedigree and Pedigree Import Wizard

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 552g-553
Author(s):  
Shahrokh Khandizadeh
Keyword(s):  
Additional Data ◽  
File Format ◽  
Fruit Crops ◽  
Operating Environment ◽  
Agronomic Characteristics ◽  
Link Type ◽  
Plant Characteristics ◽  
User Friendly

Pedigree for Windows is a user-friendly program that allows the user to trace agronomic characteristics, draw pedigrees, and view images of several fruit crops, including more than 1400 apple, 800 strawberry, 800 almond, 100 blackberry, 80 blueberry, 790 pear, 200 raspberry examples. Pedigree Import Wizard®© for Windows is an add-on software for users who are interested in importing their research or breeding data records of fruit, flower, and plant characteristics and any related images into Pedigree for Windows. Pedigree for Windows and Pedigree Import Wizard have been designed so that a user familiar with the Windows operating environment should have little need to refer to the documentation provided with the program. Pedigree Import Wizard uses a comma-separated value (csv) file format under the MS Excel environment. This option allows the user to add or import additional data to the existing database that are already stored in other software such as Lotus, Excel, Access, QuattroPro, WordPerfect, and MS Word tables, etc., as long as they work under the Windows environment. A free demo version of Pedigree and Pedigree Import Wizard for Windows is available from http://www.pgris.com.

Clustered Iconography: A Resurrected Method for Representing Multidimensional Data

2020 ◽  
pp. 004912412091494
Author(s):  
Olav Muurlink ◽  
Anthony M. Gould ◽  
Jean-Etienne Joullié
Keyword(s):  
Twentieth Century ◽  
Open Source ◽  
Multidimensional Data ◽  
Statistical Techniques ◽  
Graphical Representations ◽  
Graphical Methods ◽  
History Of ◽  
Research Findings

Development of graphical methods for representing data has not kept up with progress in statistical techniques. This article presents a brief history of graphical representations of research findings and makes the case for a revival of methods developed in the early and mid-twentieth century, notably ISOTYPE and Chernoff’s faces. It resurrects and improves a procedure, clustered iconography, which enables the presentation of multidimensional data through which readers engage more effectively with the presentation’s central message by way of an easier understanding of relationships between variables. The proposed technique is especially well adapted to the needs and protocols of open-source research.

MetaADEDB 2.0: a comprehensive database on adverse drug events

2020 ◽  
Author(s):  
Zhuohang Yu ◽  
Zengrui Wu ◽  
Weihua Li ◽  
Guixia Liu ◽  
Yun Tang
Keyword(s):  
Safety Assessment ◽  
Adverse Drug Events ◽  
Adverse Event Reporting System ◽  
Adverse Event Reporting ◽  
Supplementary Information ◽  
Online Database ◽  
Web Interface ◽  
Drug Discovery And Development ◽  
Comprehensive Information ◽  
User Friendly

Abstract Summary MetaADEDB is an online database we developed to integrate comprehensive information on adverse drug events (ADEs). The first version of MetaADEDB was released in 2013 and has been widely used by researchers. However, it has not been updated for more than seven years. Here, we reported its second version by collecting more and newer data from the U.S. FDA Adverse Event Reporting System (FAERS) and Canada Vigilance Adverse Reaction Online Database, in addition to the original three sources. The new version consists of 744 709 drug–ADE associations between 8498 drugs and 13 193 ADEs, which has an over 40% increase in drug–ADE associations compared to the previous version. Meanwhile, we developed a new and user-friendly web interface for data search and analysis. We hope that MetaADEDB 2.0 could provide a useful tool for drug safety assessment and related studies in drug discovery and development. Availability and implementation The database is freely available at: http://lmmd.ecust.edu.cn/metaadedb/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals VIP-HL: Semi-automated ACMG/AMP variant interpretation platform for genetic hearing loss

2020 ◽  
Author(s):  
Jiguang Peng ◽  
Jiale Xiang ◽  
Xiangqian Jin ◽  
Junhua Meng ◽  
Nana Song ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Expert Panel ◽  
Sequence Variant ◽  
Variant Interpretation ◽  
Web Interface ◽  
Online Tool ◽  
Genetic Hearing Loss ◽  
Genetics And Genomics ◽  
Evidence Based Guidelines ◽  
User Friendly

The American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG/AMP) have proposed a set of evidence-based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL-EP) introduced further specifications into the ACMG/AMP framework for genetic hearing loss. This study developed a tool named VIP-HL, aiming to semi-automate the HL ACMG/AMP rules. VIP-HL aggregates information from external databases to automate 13 out of 24 ACMG/AMP rules specified by HL-EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7. We benchmarked VIP-HL using 50 variants where 83 rules were activated by the ClinGen HL-EP. VIP-HL concordantly activated 96% (80/83) rules, significantly higher than that of by InterVar (47%; 39/83). Of 4948 ClinVar star 2+ variants from 142 deafness-related genes, VIP-HL achieved an overall variant interpretation concordance in 88.0% (4353/4948). VIP-HL is an integrated online tool for reliable automated variant classification in hearing loss genes. It assists curators in variant interpretation and provides a platform for users to share classifications with each other. VIP-HL is available with a user-friendly web interface at http://hearing.genetics.bgi.com/.

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