scholarly journals Spark: A navigational paradigm for genomic data exploration

2012 ◽  
Vol 22 (11) ◽  
pp. 2262-2269 ◽  
Author(s):  
C. B. Nielsen ◽  
H. Younesy ◽  
H. O'Geen ◽  
X. Xu ◽  
A. R. Jackson ◽  
...  
Keyword(s):  
Genomic Data ◽  
Data Exploration

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

2017 ◽  
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]

scholarly journals TcruziKB: Enabling Complex Queries for Genomic Data Exploration

2008 ◽  
Author(s):  
Pablo N. Mendes ◽  
Bobby McKnight ◽  
Amit P. Sheth ◽  
Jessica C. Kissinger
Keyword(s):  
Genomic Data ◽  
Data Exploration ◽  
Complex Queries

scholarly journals CoolBox: a interactive genomic data explorer for Jupyter Notebook

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.

Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

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.

scholarly journals Population genomic data in spider mites point to a role for local adaptation in shaping range shifts

2020 ◽  
Vol 13 (10) ◽  
pp. 2821-2835
Author(s):  
Lei Chen ◽  
Jing‐Tao Sun ◽  
Peng‐Yu Jin ◽  
Ary A. Hoffmann ◽  
Xiao‐Li Bing ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Genomic Data ◽  
Spider Mites ◽  
Range Shifts ◽  
Population Genomic

scholarly journals Author Correction: The NCI Genomic Data Commons

2021 ◽  
Author(s):  
Allison P. Heath ◽  
Vincent Ferretti ◽  
Stuti Agrawal ◽  
Maksim An ◽  
James C. Angelakos ◽  
...  
Keyword(s):  
Genomic Data ◽  
Data Commons
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