Unlock your biological data

?

Try: RNA sequencing CRISPR Genomic databases DESeq

Data visualization

Visualize differential gene expression with ViDGER

Differential gene expression (DGE) analysis is one of the most common applications of RNA-seq data. This process allows for the elucidation of differentially expressed genes (DEGs) across two or more conditions. Interpretation of the DGE results can be non-intuitive and time-consuming due to the variety of formats based on the tool of choice and the numerous pieces of information provided in these results files. To address this challenge, Adam McDermaid and his colleagues from South Dakota State University have developed ViDGER. Here, they present their tool and its main features.   Interpretation and Visualization of Differential Gene Expression through ViDGER   One of the most straightforward ways to gain a broader understanding of the tens-of-thousands of pieces of information generated …

Read this post
comment
0

Your top 3 venn diagram tools

Venn diagrams are very simple, yet incredibly useful tools used to show all logical relations between finite collections of different sets of data. In Venn diagrams, sets of data are often represented as overlapping circles. Data that are shared between two different sets will reside at the intersection, while unique data remain outside the intersection. Venn diagrams in biology In biology and omics, Venn diagrams can be used for a variety of purposes, such as the comparison of different lists of genes or proteins (generally 2 or 3) to identify similarities and represent them in two dimensions. Most softwares allow easy extraction of the data, and let you customize the diagrams.   Continuing our series of data visualization tools, OMICtools …

Read this post
comment
2

Your top 3 heatmap generation tools

Heatmaps are one of the most commonly used representation tools for synthesis of complex pools of data. By coding numerical values into colors, heatmaps enable quick representation of quantitative differences in expression levels of biological data. Using heatmaps to visualize your data Heatmaps are particularly useful for analysis of gene expression microarray data. Most heatmap representations are also combined with clustering methods to group genes and/or samples based on their expression patterns. Each gene is represented as a row and is color-coded to represent the intensity of its variation (either positive or negative) relative to a reference value. Biological samples are represented as columns in the grid. To evaluate the OMICtools series of data visualization tools, we asked members of the …

Read this post
comment
2

Your top 3 circos plot generation tools

Making great images of your data With the growing amount of biological data generated, innovative bioinformatics tools have been developed for modelling and synthetizing complex information in comprehensive figures. Several infographics types are now available for an informative and clear representation and analysis of your data, and which differ depending on the specific domain and question you are studying. So how do you choose the best tools to efficiently explore your data and illustrate your scientific findings? To help you answer this key question, we have initiated a series of surveys with users on the main categories of data visualization tools among those which are most used by the OMICtools community. The first of our survey series concerns the Circos plot generation tools. …

Read this post
comment
0

How to visualize your data using R

Data visualization and R Data visualization is one of the key steps of any data science related process. There are hundreds of possibilities available when it comes to visualizing data, and choosing and using the right one are determining factors in accurately getting your message across. R programming language is one of the most common tools used for this process. R is fabulous for creating charts. It allows you to create all types of visualizations and lots of libraries are developed to help users scan them quicker. However, it can sometimes be challenging – and extremely frustrating – to look for the right code to compute a desired plot. The R Graph Gallery by its creator, Yan Holtz The R graph …

Read this post
comment
0
< Previous 1 Next >

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.