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- Transcriptomics Module
BioBam Blog Categories
BioBam Blog Articles
- The Influence of Clustering Quality on Cell Type Prediction Accuracy
- Join & Call vs. Call & Join: Poster at ISMB/ECCB2025
- BioBam at the LongTREC Summer School
- Differences between Fisher’s Exact Test and GSEA for Functional Enrichment
- Reference-free analysis of long-read RNA sequencing for non-model species
- OmicsBox in a New Scientific Publication on Sorghum Stress Responses
- LongTREC Secondments at BioBam: Advancing Long-Read Transcriptomics Through Collaboration
- Cell Type Prediction with CellKb
- OmicsBox 3.4: CellKb’s Advanced Cell-Type Annotation
- BioBam Joins BIOVALSA: Innovative Valorization of Plant Biomass Waste in Valencia for Functional Bioplastic Production
- BioBam at LongTREC meeting in Sweden
- OmicsBox in SEBiBC First Congress: End-to-end Single Cell Data Analysis Poster
- Genome Completeness Assessment with BUSCO
- New Taxonomy Databases in OmicsBox
- Combining Transcriptomes with TAMA Merge
- Understanding maSigPro Timecourse Results
- OmicsBox 3.3 Release
- End-to-End Analysis of Long Reads in OmicsBox
- Cutting-Edge Long-Read Transcriptomics Research Published in Nature Methods
- Single Cell RNA-Seq analysis of Arabidopsis thaliana roots
- Population Structure Analysis with OmicsBox
- IsoQuant: Long-Read Isoform Identification and Quantification
- OmicsBox 3.2 Release
- Using BWA for DNA and RNA Alignment in OmicsBox
- Differences Between GTF and GFF Files in Genomic Data Analysis
- Tips to manage my OmicsBox subscription users
- BioBam Achieves ISO 27001 Recertification
- BioBam Trip to PAG in San Diego
- Gene Set Analysis of GWAS data with MAGMA
- Long-Read Sequence Alignment with Minimap2
- STARsolo Single-cell Quantification in OmicsBox
- Demultiplexing with Cutadapt in OmicsBox
- Monocle3 in OmicsBox: scRNA Seq trajectory interference
- BioBam organizes Single-Cell Course
- New Release of OmicsBox 3.1
- Biobam’s Sustainable Journey to ISMB/ECCB 2023
- BioBam Student Scholarship – Apply Now!
- Pathway Analysis with OmicsBox: Analyzing a Salamander Limb Regeneration Transcriptomics Dataset
- BioBam at the BIO-IT World 2023
- Decoding Long-Read Sequenced Transcriptomes: FLAIR vs. StringTie2
- Genetic Variation Exploration in Non-Model Organisms with OmicsBox
- GWAS with OmicsBox
- KEGG Pathways in OmicsBox
- Quality Assessment of DNA-Seq De Novo Assemblies using QUAST
- LongTREC – BioBam member of a new ITN initiative
- OmicsBox 3.0 Release: New Module and Features
- BioBam Team at PAG30 in San Diego
- Predict coding regions within transcripts in OmicsBox with TransDecoder
- OmicsBox Sign-Up Activation Tutorial
- OmicsBox won’t start on Ubuntu Linux
- BioBam is part of INTERCEPT-MDS, a European ITN
- Generate Gene Venn Diagram Representations with OmicsBox
- BioBam’s Commitment to Data Security: ISO 27001 Certification
- How to rename the sequence name in OmicsBox
- Cell-Type Identification via Functional Enrichment Analysis of Single-Cell RNA-Seq Data
- BioBam at the ECCB 2022
- OmicsBox 2.2 Release
- Tutorial: Single-Cell RNA-Seq Differential Expression Analysis
- BAM File Quality Control
- scRNA-seq Differential Expression with EdgeR
- Quality Assessment with LongQC
- Transcriptome Analysis with SQANTI3
- Dynamics of bacterial resistome associated based on metagenomics analysis
- Bioinformatic analysis of gene expressions involved in berries growth
- Mining Genes involved in Biodegradation of Tannery Wastes
- Biobam receives a grant from the Valencian Innovation Agency – AVI
- rRNA Removal with SortMeRNA in OmicsBox
- Metagenomics Contaminant Removal with Bowtie
- IsoSeq De-Novo Isoform Discovery with OmicsBox
- Eukaryotic Gene Finding with OmicsBox
- Single Cell Clustering With Seurat in OmicsBox
- Combined Pathway Analysis with OmicsBox
- OmicsBox Update Version 2.0
- New OmicsBox Login Dialog
- Metagenomics based In Silico Analysis of Antibiotic Resistome in Saltern
- InterProScan with Blast2GO: How to make it work again
- Metatranscriptomics Analysis of Macaques with Idiopathic Chronic Diarrhea (ICD)
- Transcriptome analysis reveals important metabolic pathways of Allium sativum
- CloudBlast and Cloud Units: How to use resources wisely
- OmicsBox Update Version 1.4
- The functional annotation of the plant Moringa oleifera
- COVID-19 Research Project in the US with OmicsBox Support
- Zeroing in on genes involved in courtship song variation in Laupala crickets
- Clustering redundant transcripts in OmicsBox with CD-HIT
- Long-Reads Assembly with OmicsBox
- OmicsBox Update Version 1.3
- De novo transcriptome analysis in Datura metel
- COVID-19 Research Project in India with OmicsBox Support
- COVID-19 Research Project with OmicsBox Support
- Unlink an OmicsBox subscription from all associated computers
- COVID-19 Research Project in Tunisia with OmicsBox Support
- COVID-19 Research Project in Brazil with OmicsBox Support
- Identification and Expression analysis of genes involved in endodormancy break in potato.
- Metagenomic analysis of two soda lakes, with and without cyanobacterial bloom, with OmicsBox
- Comparing taxonomic and functional compositions in metagenomic samples
- De novo genome assembly and annotation of fungus in OmicsBox
- Draft genome of a new Verminephrobacter eiseniae strain
- Exploring transcriptome completeness in OmicsBox with BUSCO
- Hybrid Genome Assembly in OmicsBox with SPAdes
- How to run Blast of the differential expressed genes?
- New Genome Analysis Features
- New Transcriptomics Features
- New Metagenomics Features
- Transcriptomic response of A. galli to an anthelmintic drug
- Metagenomic analysis of microbial communities with OmicsBox
- How to cite OmicsBox, Blast2GO and all available features
- Multilocus Sequence Typing MLST Analysis Tool
- How to create a taxonomic mapping file.
- OmicsBox Example Datasets
- Introductory promotion of our new Metagenomics Module
- Transcriptome analysis of Acinetobacter baumannii cells under different conditions
- BioBam Student Scholarship – Apply Now!
- BioBam at the 6th Microbiome R&D Forum in Rotterdam
- Introducing the BioBam account
- Release of OmicsBox v.1.1
- BioBam at the BioIT April 2019
- Combine differential expression results with functional annotation in OmicsBox
- Lipid transcriptome profiling of indigenous Dunaliella sp. isolate
- Interview with Mariana Monteiro
- Whole Genome Functional Annotation of Solanum lycopersicum
- BioBam at PAG January 2019
- How to export Gene Finder GFF output with GO terms.
- Expression quantification and differential expression analysis
- Learn about de-novo transcriptome assembly
- Basic Transcriptome Characterization with Blast2GO
- Enrichment Analysis from pairwise differential expression results in OmicsBox
- Improve functional annotations using “Retrieve Blast Top-hit”
- How to create a gene list within OmicsBox to run the functional enrichment analysis
- How to change sequence names coming from Prokaryotic GeneFinding
- New RNA-Seq Features in Blast2GO 5
- Load Sequences and Annotation from a list of identifiers
- Load FASTA sequences from Reference and GFF file
- How to combine two projects in OmicsBox
- Blast2GO poster exhibited at ECCB 2018
- NGS Preprocessing and Quality Control: How-To with OmicsBox
- Gene expression profiling in fresh-water colonial green alga Volvox carteri
- Release Version 5.2
- How to create analysis workflows
- Expression Estimation at Transcript-Level
- Is Repeat-Masking necessary in Blast2GO?
- Evolutionary analysis of three Pneumocystis genomes
- Gene expression study of peacock blenny Salaria pavo
- Expression Quantification at Gene-Level
- A basic evaluation of the Coding-Potential Assessment Tool
- White sequences in CloudBlast and CloudIPS
- Release Version 5
- Coding Potential Assessment Tool
- Changes in Maize Transcriptome due to Virus Infection
- Run blast icon greyed out in OmicsBox
- Enrichment analysis on 2 groups of sequences
- NCBI GenBank Submission
- Time-Course Differential Expression Analysis
- Evaluation of Eukaryotic Gene Finding with Augustus in OmicsBox
- Pairwise Differential Expression Analysis
- Time Course Expression Analysis
- Pairwise Differential Expression Analysis
- How to translate longest ORFs
- Major Release Version 4
- Functional Analysis of Pancreatic Cancer Expression Profiles
- How to perform a Gene Set Enrichment Analysis (GSEA)
- How to use PSORTb
- Coloured Graphs: How to combine multiple functional GO profiles
- How to select sequences by function and create ID lists
- How to perform a Fisher’s Exact Test
- How to use BioMart and GO-Slim
- How to run local Blast against a custom database
- How to use RFAM
- How to Set Maximum Memory for Blast2GO
- How to Change the Temp Folder Location for Blast2GO
- Analysis Progress Chart
- Tutorial: some parts of the application are not working.
- How to run Blast2GO installer in Linux systems?
- How to install OmicsBox on a shared workstation with multiple user access?
- New Version 3.3
- New Version 3.2
- Error when running LocalBlast “NCBI Binaries C++ Exception”.
- Brief review: Gene-Finding for Bacterial Genomes
- Reformat Uniprot/Swissprot Species Distribution
- Blast2GO PRO Plugin for CLC bio Genomics Workbench Update
- Run Local Blast within OmicsBox
- Blast2GO Command Line Features 1.1.4
- Command Line Examples
- Blast2GO Release Version 3.1
- BioBam and Biomatters: Functional Annotation Tools for Geneious
- How to create a custom NCBI Blast Database from a FASTA File
- CLC bio and BioBam Deliver De-Novo Genome Workflow
