Use Cases, Reviews, Tutorials

Product Tutorial, Quickstarts, New Features, etc.

Pathway Analysis with OmicsBox: Analyzing a Salamander Limb Regeneration Transcriptomics Dataset

The functional interpretation of differentially expressed genes obtained from RNA-seq data is a critical step in elucidating the intricate biological mechanisms underlying complex biological processes. Pathway analysis has emerged as a powerful approach to gaining insights into the coordinated interactions among genes within biological pathways. However, a major challenge in pathway analysis lies in the availability of annotation data, which

Read More »

Decoding Long-Read Sequenced Transcriptomes: FLAIR vs. StringTie2

Transcriptome reconstruction is a challenging bioinformatic problem. The development of long-read sequencing technologies has made it easier to solve this issue thanks to the possibility to have transcripts entirely contained in a read. In addition, different algorithms have emerged to generate transcriptomes from long-read datasets, such as FLAIR and StringTie2. Both tools can be used for transcriptome reconstruction with long-read data.

Read More »
genetic variaton

Genetic Variation Exploration in Non-Model Organisms with OmicsBox

The study of genetic variation is fundamental in genomics research as it enables the comprehension of mutation causes and effects in the diversity of life. However, research in this field is well-developed in model organisms, while non-model organisms lack sufficient guidance for a consistent variant analysis pipeline. OmicsBox serves as a robust tool for investigating genetic variation in non-model organisms,

Read More »

Demultiplexing with Cutadapt in OmicsBox

Barcoding and demultiplexing in high-throughput sequencing experiments Barcoding, or indexing, is a widely used strategy in high-throughput sequencing experiments. This method enables the multiplexing of numerous samples in a single sequencing run by adding a unique DNA sequence to each sample before sequencing. During sequencing, the barcodes are read along with the DNA fragments, allowing the identification and split of

Read More »
Easy GWAS with OmicsBox

GWAS with OmicsBox

Genome-Wide Association Studies (GWAS) is a valuable approach to investigating the relationship between genetic variations and phenotypic traits. However, due to many different analysis options, performing GWAS can be challenging, especially for researchers without a strong background in statistics or bioinformatics. OmicsBox’s Genetic Variation Module provides a solution by offering a user-friendly interface to powerful analysis tools. It includes a

Read More »

Quality Assessment of DNA-Seq De Novo Assemblies using QUAST

Genetic Variation studies often involve analyzing samples from a previously studied species. For instance, it is of interest to examine genomes of various cultivars, strains, or populations of the same species. In such cases, it may be necessary to perform de novo DNA-Seq assembly to obtain the genome of the sequenced organisms, even if a reference genome is available. To

Read More »

Cell-Type Identification via Functional Enrichment Analysis of Single-Cell RNA-Seq Data

  Single-cell RNA sequencing (scRNA-seq) has proven its usefulness in deciphering biological processes. Since it allows the study of samples at the cell level, it provides a more detailed view of the underlying biology.  A nearly mandatory step in any scRNA-seq analysis is to identify the cell types present in the analyzed samples so further biological insights can be obtained.

Read More »

Blog Categories:


Releases, Media, Announcements, etc.

Tips And Tricks

Mini-tutorials for common use-cases and to address frequently asked questions FAQs

Video Tutorials

Helpful Features, Tips and Tricks

Use Cases, Reviews, Tutorials

Product Tutorial, Quickstarts, New Features, etc.

Most Popular: