transcriptomics Archives - Page 2 of 3

New Transcriptomics Features

Carlos Menor October 25, 2019

Release OmicsBox version 1.2 (24th of October, 2019) We are happy to announce the following updates for the transcriptomics module. New features include Completeness Assessment and Predict Coding Regions. More details can be found below as well as in the online user manual and Transcriptomics Module website. Completeness Assessment The Completeness Assessment functionality provides quantitative measures for the assessment of transcriptome assembly completeness, based on

Transcriptomic response of A. galli to an anthelmintic drug

Jesus Gutierrez October 24, 2019

In this analysis, we will reproduce a study carried out by Michaela M. Martis et al. in 2017 with OmicsBox. (http://doi.org/10.1371/journal.pone.0185182) Introduction Ascaridia galli is an intestinal parasite that infects a wide range of domestic birds. It is especially important in European farms, where it parasites laying hens and causes economic problems. The only available treatments are the Benzimidazole derivatives,

Multilocus Sequence Typing MLST Analysis Tool

Carlos Menor July 29, 2019

The Multilocus Sequence Typing Analysis Tool of OmicsBox (MLST) is a nucleotide sequence-based approach of characterizing isolates of bacterial species using the sequences of internal fragments of seven housekeeping genes. This video shows step-by-step how to analyze bacterial sequences with the MLST App in OmicsBox. As input, users can provide either DNA-Seq reads in FASTQ or contigs/scaffolds in FASTA format.

OmicsBox Video Introduction

Stefan Götz July 9, 2019

This 5-minute video provides a brief introduction to OmicsBox. All main features of all modules are introduced. OmicsBox is a bioinformatics Solution to easy your Omcis Data Analysis. Our workflows get you from raw reads tp insights fast and easy. The presented modules include Transcriptomics, Functional Annotation and Analysis with Blast2GO, the Genome Analysis Module as well as the Metagenomics

Transcriptome analysis of Acinetobacter baumannii cells under different conditions

Mariana Monteiro June 11, 2019

OmicsBox Supported Project Researchers: Background and Project Overview: A.baumannii, a nosocomial pathogen, ranks first in the WHO’s list of antibiotic-resistant priority pathogen. The problem of increasing frequency of multi-drug resistance in A. baumannii has been further compounded by tolerance to high concentration of antibiotics due to persister cells. Persister cells are phenotypic variants of normal cells that are formed in

Combine differential expression results with functional annotation in OmicsBox

Jesus Gutierrez April 18, 2019

Once differential expression results are retrieved, it could be interesting to assign functional annotations to the differentially expressed genes and visualize the results in a single project. This is possible in OmicsBox.

BioBam at PAG January 2019

Stefan Götz January 22, 2019

We attended PAG XXVII, the largest Ag-Genomics Meeting in the world. https://www.intlpag.org/30/ We launched OmicsBox Beta and gave away a whole bunch of free subscriptions. Here are a few pics of the happy winners! Hopefully, they took advantage. The PAG 2019 Team with our new OmcisBox Booth :-). See you next year!

Basic Transcriptome Characterization with Blast2GO

Jesus Gutierrez November 13, 2018

Analysis workflow Objective: To describe the process of a transcriptome characterization using Blast2GO. Input data: A mouse RNA-seq dataset composed of 140803 contigs. Pipeline: Blastx and InterproScan were performed with the complete dataset to identify proteins. Sequences with no Blastx hits nor IPS results were selected and further analyzed. RFAM and Local Blast (against an EST mouse db) were performed with the sequences with

Release Version 5.2

Mariana Monteiro August 8, 2018

(Release Date: 02/08/2018) We are happy to announce that Blast2GO 5.2 has now been released. This update makes our bioinformatics tool for straightforward functional genomics even better.Read below to learn which features and improvements are part of this release. Main features: Venn Diagrams that are fully customizable and allows multiple list comparisons FastQ Pre-Processing (Adapters, Quality, Length) with multiple trimming options.

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New Transcriptomics Features

Transcriptomic response of A. galli to an anthelmintic drug

Multilocus Sequence Typing MLST Analysis Tool

OmicsBox Video Introduction

Transcriptome analysis of Acinetobacter baumannii cells under different conditions

Combine differential expression results with functional annotation in OmicsBox

BioBam at PAG January 2019

Basic Transcriptome Characterization with Blast2GO

Release Version 5.2

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