Tag: Exploration

Panache v1.0.0 – PANgenome Analyzer with CHromosomal Exploration

Panache v1.0.0

:: DESCRIPTION

Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.

::DEVELOPER

Panache team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Durant É, Sabot F, Conte M, Rouard M.
Panache: a Web Browser-Based Viewer for Linearized Pangenomes.
Bioinformatics. 2021 Oct 2:btab688. doi: 10.1093/bioinformatics/btab688. Epub ahead of print. PMID: 34601567.

MaGnET 2.0 – Malaria Genome Exploration Tool

MaGnET 2.0

:: DESCRIPTION

MaGnET is a software tool enabling intuitive ‘exploration-style’ visualization of functional genomics data relating to the malaria parasite, Plasmodium falciparum.

::DEVELOPER

MaGnET team

:: SCREENSHOTS

MaGnET

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MaGnET

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Sep 15;29(18):2350-2. doi: 10.1093/bioinformatics/btt384. Epub 2013 Jul 27.
MaGnET: Malaria Genome Exploration Tool.
Sharman JL1, Gerloff DL.

imDEV 1.4.2 – omics data exploration and visualization in Excel

imDEV 1.4.2

:: DESCRIPTION

imDEV (Interactive modules for Data Exploration and Visualization) is a Microsoft Excel spreadsheet embedded application providing an integrated environment for the analysis of omics data through a user-friendly interface. Individual modules enable interactive and dynamic analyses of large data by interfacing R’s multivariate statistics and highly customizable visualizations with the spreadsheet environment, aiding robust inferences and generating information rich data visualizations. This tool provides access to multiple comparisons with false discovery correction, hierarchical clustering, principal (PCA) and independent component analyses (ICA), partial least squares regression (PLS) and discriminant analysis (PLS-DA), through an intuitive interface for creating high quality two and a three-dimensional visualizations including scatter plot matrices, distribution plots, dendrograms, heat maps, biplots, trellis biplots and  correlation networks.

::DEVELOPER

Dmitry Grapov

:: SCREENSHOTS

imDEV

:: REQUIREMENTS

  •  Excel
  • R package

:: DOWNLOAD

 imDEV

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2288-90. doi: 10.1093/bioinformatics/bts439. Epub 2012 Jul 18.
imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel.
Grapov D, Newman JW.

Elviz 2.0 – Exploration of Metagenomic Assemblies

Elviz 2.0

:: DESCRIPTION

Elviz (Environmental Laboratory Visualization) is an interactive web-based tool for the visual exploration of assembled metagenome data and their complex metadata.

:: DEVELOPER

Joint Genome Institute (JGI).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web  browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Elviz – exploration of metagenome assemblies with an interactive visualization tool.
Cantor M, Nordberg H, Smirnova T, Hess M, Tringe S, Dubchak I.
BMC Bioinformatics. 2015 Apr 28;16(1):130.

Sibelia 3.0.7 – Synteny Block ExpLoration tool

Sibelia 3.0.7

:: DESCRIPTION

Sibelia is a comparative genomic tool。 It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments.

::DEVELOPER

Algorithmic Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Windows

:: DOWNLOAD

 Sibelia

:: MORE INFORMATION

Citation

F1000Res. 2013 Nov 25;2:258. doi: 10.12688/f1000research.2-258.v1. eCollection 2013.
C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison.
Minkin I, Pham H, Starostina E, Vyahhi N, Pham S

Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham.
Sibelia: A fast synteny blocks generation tool for many closely related microbial genomes
(submitted)

MARRVEL v2 – Model organism Aggregated Resources for Rare Variant ExpLoration

MARRVEL v2

:: DESCRIPTION

MARRVEL aims to facilitate the use of public genetic resources to prioritize rare human gene variants for study in model organisms. To automate the search process and gather all the data in a simple display we extract data from human data bases (OMIM, ExAC, Geno2MP, DGV, and DECIPHER) for efficient variant prioritization. The protein sequences for six organisms (S. cerevisiae, C. elegans, D. melanogaster, D. rerio, M. musculus, and H. sapiens) are aligned with highlighted protein domain information via collaboration with DIOPT.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Wang J, Al-Ouran R, Hu Y, Kim SY, Wan YW, Wangler MF, Yamamoto S, Chao HT, Comjean A, Mohr SE; UDN, Perrimon N, Liu Z, Bellen HJ.
MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.
Am J Hum Genet. 2017 Jun 1;100(6):843-853. doi: 10.1016/j.ajhg.2017.04.010. Epub 2017 May 11. PMID: 28502612; PMCID: PMC5670038.

NetConfer – Exploration and Comparisons of Biological Networks

NetConfer

:: DESCRIPTION

NetConfer is a web based tool designed for comparative analysis of multiple interaction networks. It implements various analysis methods organized as workflows.

::DEVELOPER

NetConfer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nagpal S, Baksi KD, Kuntal BK, Mande SS.
NetConfer: a web application for comparative analysis of multiple biological networks.
BMC Biol. 2020 May 19;18(1):53. doi: 10.1186/s12915-020-00781-9. Erratum in: BMC Biol. 2020 Oct 22;18(1):147. PMID: 32430035; PMCID: PMC7236966.

AnnotCompute – Annotation-based Exploration and Meta-analysis of Genomics Experiments

AnnotCompute

:: DESCRIPTION

AnnotCompute is an information discovery platform for repositories of functional genomics experiments such as ArrayExpress.

::DEVELOPER

the Computational Biology and Informatics Laboratory at the University of Pennsylvania

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

Database (Oxford). 2011 Dec 21;2011:bar045. doi: 10.1093/database/bar045.
AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments.
Zheng J, Stoyanovich J, Manduchi E, Liu J, Stoeckert CJ Jr.

STEPP – Search Tool for Exploration of Petri net Paths

STEPP

:: DESCRIPTION

STEPP is a tool programmed to performe paths searchs in (metabolic) petri nets.

::DEVELOPER

Molecular Bioinformatics MolBI

:: SCREENSHOTS

STEPP1

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 STEPP

:: MORE INFORMATION

Citation

In Silico Biol. 2005;5(2):129-37.
STEPP–Search Tool for Exploration of Petri net Paths: a new tool for Petri net-based path analysis in biochemical networks.
Koch I1, Schueler M, Heiner M.

CummeRbund 2.28.0 – Exploration, Analysis and Visualization of Cufflinks high-throughput RNA-Seq data

CummeRbund 2.28.0

:: DESCRIPTION

CummeRbund is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output.CummeRbund was designed to help simplify the analysis and exploration portion of RNA-Seq data derrived from the output of a differential expression analysis using cuffdiff with the goal of providing fast and intuitive access to your results.

::DEVELOPER

Kellis Lab &  the Rinn Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

 CummeRbund

:: MORE INFORMATION

Citation

Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016.
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L.