VennDIS: A JavaFX-based Venn and Euler diagram software to generate publication quality figures

PROTEOMICS ◽  
2015 ◽  
Vol 15 (7) ◽  
pp. 1239-1244 ◽  
Author(s):  
Vladimir Ignatchenko ◽  
Alexandr Ignatchenko ◽  
Ankit Sinha ◽  
Paul C. Boutros ◽  
Thomas Kislinger
Keyword(s):  
Euler Diagram ◽  
Publication Quality

Small Computer System for Micrograph Analysis

1981 ◽  
Vol 39 ◽  
pp. 270-271
Author(s):  
J. F. Hainfeld ◽  
J. S. Wall
Keyword(s):  
Large Range ◽  
Small Computer ◽  
Black And White ◽  
Contour Maps ◽  
Points Of Interest ◽  
Computer Aided Analysis ◽  
Specialized Hardware ◽  
Additional Memory ◽  
Selection Of ◽  
Publication Quality

Cost reduction and availability of specialized hardware for image processing have made it reasonable to purchase a stand-alone interactive work station for computer aided analysis of micrographs. Some features of such a system are: 1) Ease of selection of points of interest on the micrograph. A cursor can be quickly positioned and coordinates entered with a switch. 2) The image can be nondestructively zoomed to a higher magnification for closer examination and roaming (panning) can be done around the picture. 3) Contrast and brightness of the picture can be varied over a very large range by changing the display look-up tables. 4) Marking items of interest can be done by drawing circles, vectors or alphanumerics on an additional memory plane so that the picture data remains intact. 5) Color pictures can easily be produced. Since the human eye can detect many more colors than gray levels, often a color encoded micrograph reveals many features not readily apparent with a black and white display. Colors can be used to construct contour maps of objects of interest. 6) Publication quality prints can easily be produced by taking pictures with a standard camera of the T.V. monitor screen.

scholarly journals Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

2014 ◽  
Vol 30 (19) ◽  
pp. 2808-2810 ◽  
Author(s):  
D. H. Phanstiel ◽  
A. P. Boyle ◽  
C. L. Araya ◽  
M. P. Snyder
Keyword(s):  
Publication Quality

scholarly journals SparK: A Publication-quality NGS Visualization Tool

2019 ◽  
Author(s):  
Stefan Kurtenbach ◽  
J. William Harbour
Keyword(s):  
Standard Deviation ◽  
Ucsc Genome Browser ◽  
Genomic Region ◽  
Visualization Tool ◽  
Command Line ◽  
Integrative Genomics ◽  
Rna Seq ◽  
Vector Graphic ◽  
Ngs Data ◽  
Publication Quality

AbstractWhile there are sophisticated resources available for displaying NGS data, including the Integrative Genomics Viewer (IGV) and the UCSC genome browser, exporting regions and assembling figures for publication remains challenging. In particular, customizing track appearance and overlaying track replicates is a manual and time-consuming process. Here, we present SparK, a tool which auto-generates publication-ready, high-resolution, true vector graphic figures from any NGS-based tracks, including RNA-seq, ChIP-seq, and ATAC-seq. Novel functions of SparK include averaging of replicates, plotting standard deviation tracks, and highlighting significantly changed areas. SparK is written in Python 3, making it executable on any major OS platform. Using command line prompts to generate figures allows later changes to be made very easy. For instance, if the genomic region of the plot needs to be changed, or tracks need to be added or removed, the figure can easily be re-generated within seconds without the manual process of re-exporting and re-assembling everything. After plotting with SparK, changes to the output SVG vector graphic files are simple to make, including text, lines, and colors. SparK is publicly available on GitHub: https://github.com/harbourlab/SparK.

scholarly journals Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 1750 ◽  
Author(s):  
Michael C. Ryan ◽  
Mark Stucky ◽  
Chris Wakefield ◽  
James M. Melott ◽  
Rehan Akbani ◽  
...  
Keyword(s):  
Molecular Profiling ◽  
Study Data ◽  
Linear Process ◽  
Heat Map ◽  
Web Based ◽  
Heat Maps ◽  
Map Generation ◽  
Genome Scale ◽  
Quality Maps ◽  
Publication Quality

Clustered heat maps are the most frequently used graphics for visualization and interpretation of genome-scale molecular profiling data in biology.  Construction of a heat map generally requires the assistance of a biostatistician or bioinformatics analyst capable of working in R or a similar programming language to transform the study data, perform hierarchical clustering, and generate the heat map.  Our web-based Interactive Heat Map Builder can be used by investigators with no bioinformatics experience to generate high-caliber, publication quality maps.  Preparation of the data and construction of a heat map is rarely a simple linear process.  Our tool allows a user to move back and forth iteratively through the various stages of map generation to try different options and approaches.  Finally, the heat map the builder creates is available in several forms, including an interactive Next-Generation Clustered Heat Map that can be explored dynamically to investigate the results more fully.

scholarly journals Guide to image editing and production of figures for scientific publications with an emphasis on taxonomy Image editing for scientific publications

2020 ◽  
Vol 96 (1) ◽  
pp. 139-158
Author(s):  
Marcus Bevilaqua
Keyword(s):  
Image Editing ◽  
Scientific Publications ◽  
Digital Photo ◽  
Adobe Photoshop ◽  
Photo Editing ◽  
Publication Quality

Figures for scientific publications go through various stages from the planning, to the capturing of images, to the production of finished figures for publication. This guide is meant to familiarise the reader with the main image-editing software used by professional photographers. The guide’s focus is on digital photo editing and the production of figures using Adobe Photoshop to produce publication-quality figures for scientific publications. This guide will be of fundamental use for the academic public, especially taxonomists and others who work with images. Besides, it should be useful for anyone interested in becoming familiar with the basic tools of image editing.

scholarly journals Teaching behavior technicians to create publication-quality, single-case design graphs in graphpad prism 7

2018 ◽  
Vol 51 (4) ◽  
pp. 998-1010 ◽  
Author(s):  
Daniel R. Mitteer ◽  
Brian D. Greer ◽  
Wayne W. Fisher ◽  
Victoria L. Cohrs
Keyword(s):  
Single Case ◽  
Single Case Design ◽  
Teaching Behavior ◽  
Case Design ◽  
Publication Quality

Visualization of Phage Genomic Data: Comparative Genomics and Publication-Quality Diagrams

2017 ◽  
pp. 239-260 ◽  
Author(s):  
Dann Turner ◽  
J. Mark Sutton ◽  
Darren M. Reynolds ◽  
Eby M. Sim ◽  
Nicola K. Petty
Keyword(s):  
Comparative Genomics ◽  
Genomic Data ◽  
Publication Quality
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