TcruziKB: Enabling Complex Queries for Genomic Data Exploration

karyoploteR: an R/Bioconductor package to plot customizable linear genomes displaying arbitrary data

10.1101/122838 ◽

2017 ◽

Cited By ~ 1

Author(s):

Bernat Gel ◽

Eduard Serra

Keyword(s):

Experimental Data ◽

Source Code ◽

Genomic Data ◽

Data Exploration ◽

Main Function ◽

Bioconductor Package ◽

End User ◽

Creation Process ◽

Whole Genomes ◽

Linear Genomes

AbstractMotivationData visualization is a crucial tool for data exploration, analysis and interpretation. For the visualization of genomic data there lacks a tool to create customizable non-circular plots of whole genomes from any species.ResultsWe have developed karyoploteR, an R/Bioconductor package to create linear chromosomal representations of any genome with genomic annotations and experimental data plotted along them. Plot creation process is inspired in R base graphics, with a main function creating karyoplots with no data and multiple additional functions, including custom functions written by the end-user, adding data and other graphical elements. This approach allows the creation of highly customizable plots from arbitrary data with complete freedom on data positioning and representation.AvailabilitykaryoploteR is released under Artistic-2.0 License. Source code and documentation are freely available through Bioconductor (http://www.bioconductor.org/packages/karyoploteR)[email protected]

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Spark: A navigational paradigm for genomic data exploration

Genome Research ◽

10.1101/gr.140665.112 ◽

2012 ◽

Vol 22 (11) ◽

pp. 2262-2269 ◽

Cited By ~ 23

Author(s):

C. B. Nielsen ◽

H. Younesy ◽

H. O'Geen ◽

X. Xu ◽

A. R. Jackson ◽

...

Keyword(s):

Genomic Data ◽

Data Exploration

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CoolBox: a interactive genomic data explorer for Jupyter Notebook

10.1101/614222 ◽

2019 ◽

Author(s):

Weize Xu ◽

Da Lin ◽

Ping Hong ◽

Liang Yi ◽

Rohit Tyagi ◽

...

Keyword(s):

Genomic Data ◽

Application Programming Interface ◽

Data Exploration ◽

Rna Seq ◽

Sequencing Technologies ◽

Data Formats ◽

Genomic Data Visualization ◽

Application Programming ◽

Interactive Data ◽

Python Package

AbstractSummaryCoolBox is a Python package for interactive genomic data exploration based on Jupyter notebook. It provides a ggplot2-like Application Programming Interface (API) for genomic data visualization, and a Jupyter/ipywidgets based Graphical User Interface (GUI) for interactive data exploration. CoolBox is a versatile multi-omics explorer supporting most types of data formats generated by various sequencing technologies like RNA-Seq, ChIP-Seq, ChIA-PET and Hi-C.Availability and implementationCoolBox is purely implemented with Python, and the GUI widget in Jupyter notebook is based on the ipywidgets package. It is open-source and available under GPLv3 license at https://github.com/GangCaoLab/CoolBox.

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AciDB 1.0: a database of acidophilic organisms, their genomic information and associated metadata

Bioinformatics ◽

10.1093/bioinformatics/btaa638 ◽

2020 ◽

Vol 36 (19) ◽

pp. 4970-4971

Author(s):

Gonzalo Neira ◽

Diego Cortez ◽

Joaquin Jil ◽

David S Holmes

Keyword(s):

Source Code ◽

Genomic Data ◽

Tree Of Life ◽

Physiological Traits ◽

Genomic Information ◽

Growth Data ◽

Genome Sequences ◽

Genomic Features ◽

Searchable Database ◽

Complex Queries

Abstract Motivation There are about 600 available genome sequences of acidophilic organisms (grow at a pH < 5) from the three domains of the Tree of Life. Information about acidophiles is scattered over many heterogeneous sites making it extraordinarily difficult to link physiological traits with genomic data. We were motivated to generate a curated, searchable database to address this problem. Results AciDB 1.0 is a curated database of sequenced acidophiles that enables researchers to execute complex queries linking genomic features to growth data, environmental descriptions and taxonomic information. Availability and implementation AciDB 1.0 is freely available online at: http://AciDB.cl. The source code is released under an MIT license at: https://gitlab.com/Hawkline451/acidb/.

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Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.79s.1.20 ◽

2019 ◽

Vol 79 (01S) ◽

Author(s):

Pawan Kumar Jayaswal ◽

Asheesh Shanker ◽

Nagendra Kumar Singh

Keyword(s):

Evolutionary Relationship ◽

Genomic Data ◽

Gene Clusters ◽

Species Trees ◽

Model Species ◽

Tubulin Gene ◽

Tubulin Genes ◽

Eukaryotic Species ◽

Relationship Of ◽

Insight Into

Actin and tubulin are cytoskeleton proteins, which are important components of the celland are conserved across species. Despite their crucial significance in cell motility and cell division the distribution and phylogeny of actin and tubulin genes across taxa is poorly understood. Here we used publicly available genomic data of 49 model species of plants, animals, fungi and Protista for further understanding the distribution of these genes among diverse eukaryotic species using rice as reference. The highest numbers of rice actin and tubulin gene homologs were present in plants followed by animals, fungi and Protista species, whereas ten actin and nine tubulin genes were conserved in all 49 species. Phylogenetic analysis of 19 actin and 18 tubulin genes clustered them into four major groups each. One each of the actin and tubulin gene clusters was conserved across eukaryotic species. Species trees based on the conserved actin and tubulin genes showed evolutionary relationship of 49 different taxa clustered into plants, animals, fungi and Protista. This study provides a phylogenetic insight into the evolution of actin and tubulin genes in diverse eukaryotic species.

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