Unlock your biological data

?

Try: RNA sequencing CRISPR Genomic databases DESeq

OMICtools blog

Stay on top of what's going on in bioinformatics

Latest top stories

Choosing the right name for a bioinformatics tool

The name of your bioinformatics tool is the icing on the cake. You should be very attentive and feel concerned regarding this feature. While having a great name does not assure you to stand out, a bad appellation often results in a failure to reach your audience. The do’s and don’ts Don’t take a name that already exists Your tool is unique. As such, it deserves to have a sole name. Don’t try to copy the name of a famous tool or your favorite one. It can be detrimental for you. Indeed, people tend to compare products with each other, especially if they have the same title. They can be confused about the function of your tool.   OMICtools contains …

Read this post
comment
1

Improve your differential gene expression analysis with EPEE

Differential gene expression is highly common. The standard paradigm is to quantify the significance of differences in the individual gene expression values, commonly known as differential expression (DE) analysis. One opportunity to improve the widely used DE analysis is to incorporate known gene regulation relationships. Without regulatory knowledge, DE methods cannot discover any perturbation/regulation events due to post-transcriptional and/or translational mechanisms. To address this challenge, Murat Cobanoglu and his colleagues from Lyda Hill Department of Bioinformatics have developed EPEE. Here, they present their tool and its main features. EPEE features To more accurately analyze differential gene expression data, we need algorithms that account for differential regulation (DR). However, most currently existing DR methods do not strictly integrate existing knowledge of transcriptional regulation …

Read this post
comment
0

Evaluate the quality of your read alignment with GeneQC

RNA-sequencing has replaced gene array and is now the leading technology in gene expression analysis. After a sequencing step, reads need to be mapped to a reference genome. However, this step is not perfect and errors can impact all downstream analyses. To address this issue, Adam McDermaid and colleagues have developed GeneQC, a tool to evaluate the quality of read alignment. Here, he describes GeneQC and its features. Quality control of read alignment One of the main benefits of using modern RNA-Sequencing (RNA-Seq) technology is the more accurate gene expression estimations compared with previous generations of expression data, such as the microarray. However, numerous issues can result in the possibility that an RNA-Seq read can be mapped to multiple locations …

Read this post
comment
0

Explore molecular interactions across cancer types with CancerNet

Cancer is a complex disease characterized by a large number of molecular interaction alterations. Knowledge of molecular interactions is quite useful for discovering the functions of molecules and the processes they are involved in. However, there is little systematic insight into the nature and scale of the potential interactions in human cancers.     To solve this gap, Dr. Ming Chen and his colleagues from the Institute of Bioinformatics in Zhejiang University constructed CancerNet, a database for decoding multilevel molecular interactions across diverse cancer types. Here, they describe the features of CancerNet. The CancerNet database   CancerNet aims to provide cancer-specific molecular interaction networks across multiple cancer types. It includes 33 human cancer types. The interactions contain protein-protein interactions (PPIs), miRNA–target …

Read this post
comment
0

qPCR techniques and analysis software tools

Quantitative real-time polymerase chain reaction (qPCR) is widely used for the detection of specific nucleic acids, measurement of RNA transcript abundance and validation of high-throughput experimental results. While high-throughput sequencing (HTS) has revolutionized the fields of genomics and transcriptomics, qPCR techniques have evolved and can now be performed in a high-throughput fashion. Introduction qPCR is an easy-to-perform technique to evaluate the relative (or absolute) expression of genes as compared to each other and/or a reference. Traditional qPCR is often used to validate results from gene arrays or HTS, as it is more precise, rapid to perform, and cheap.   Recently, new technologies have been developed to increase the number of genes that can be tested simultaneously. Next generation qPCR platforms …

Read this post
comment
0
< Previous 1 2 3 4 5 Next >

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