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OmicsBox 3.3 Release

BioinformaticsWe are excited to announce the release of OmicsBox 3.3, the All-In-One bioinformatics software, designed to simplify your research. This latest version integrates a range of new features and improvements, offering improved usability, advanced functionalities, and expanded database support to meet the diverse needs of the bioinformatics community. With a focus on providing powerful tools and resources, OmicsBox 3.3 brings

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OmicsBox 3.2 Release

We are happy to announce the latest update of OmicsBox 3.2. “I am particularly happy to announce that with our latest release, our team managed to create a straightforward yet sophisticated solution for the challenging domain of Single Cell Transcriptomics. This marks a significant enhancement to the suite of complex analysis scenarios OmicsBox simplifies, including also Long-Read Transcriptomics, a field

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Monocle3 in OmicsBox: scRNA Seq trajectory interference

OmicsBox’s Single Cell Data Analysis encompasses a comprehensive range of steps, spanning read quantification, pre-processing, clustering, differential expression analysis, and even advanced analyses like trajectory analysis and functional enrichment. This blog post will focus on general trajectory inference using Monocle3 within OmicsBox. Pseudotime Analysis with Monocle3 Monocle3, developed by the Trapnell lab, is a scRNA-Seq data analysis toolkit written in

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New Release of OmicsBox 3.1

Empowering Researchers with Advanced End-to-End Analysis Tools for Single-Cell and Genetic Variation Studies. We’re thrilled to announce the much-anticipated arrival of OmicsBox 3.1, a release that brings significant improvements to single-cell data analysis with UMI-based technology support and introduces a functional enrichment tool for genetic variation analysis. It also enhances OmicsBox’s long-read transcriptome analysis options, making it a one-of-a-kind solution.

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omicsbox 3.0 release

OmicsBox 3.0 Release: New Module and Features

Once again we are pleased to announce the latest update of OmicsBox 3.0. The whole BioBam team has worked to bring the new version of the BioBam bioinformatics solution to life. We proudly present the Genetic Variation Module as the highlight of OmicsBox 3.0. This module enables variant calling, filtering, and annotation, as well as the association of genetic variations

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OmicsBox 2.2 Release

We are happy to announce the latest update of OmicsBox 2.2. After several months of intensive work we are finally ready to present the new version of BioBam’s bioinformatics solution. OmicsBox 2.2 comes with new Single Cell and Long Read Data Analysis Features and many other platform improvements. OmicsBox continues improving to become the most efficient, powerful and user-friendly bioinformatics

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Single-Cell Differential Expression Analysis

Tutorial: Single-Cell RNA-Seq Differential Expression Analysis

The differential expression (DE) analysis has been used in bulk RNA-seq analysis for many years. It allows us to statistically measure changes in gene expression levels between different groups. With bulk RNA-seq analysis many cells are sequenced at the same time, so gene expression levels are commonly measured at the tissue level. Thus, the differences between samples and conditions are

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BAM File Quality Control

Transcriptome sequencing (RNA-Seq) produces big amounts of valuable information on all transcribed elements in the genome. With RNA-Seq, researchers can interrogate the transcriptome to profile gene expression, uncover alternative splicing, and identify novel and discard aberrant transcripts and coding variants, among others. The resulting BAM Files are the source of information for all proceeding step

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scRNA-seq Differential Expression with EdgeR

Why Differential Expression Analysis with Single-cell RNA-seq data? The differential expression (DE) analysis has been used in bulk RNA-seq analysis for many years. It statistically measures changes in gene expression levels between different groups. With bulk RNA-seq analysis many cells are sequenced at the same time, so gene expression levels are commonly measured at the tissue level. Thus, the differences

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