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BioBam Bioinformatics
Испания
Добавлен 4 ноя 2014
BioBam is a leading bioinformatics solution provider which accelerate research in disciplines such as agricultural genomics, microbiology and environmental NGS studies, amongst others.
BioBam is committed to the development of user-friendly software solutions for biological research. Our mission is to transform complex data analysis procedures into an attractive and interactive task. BioBam is devoted to close the gap between experimental work, bioinformatics analysis and applied research.
BioBam is committed to the development of user-friendly software solutions for biological research. Our mission is to transform complex data analysis procedures into an attractive and interactive task. BioBam is devoted to close the gap between experimental work, bioinformatics analysis and applied research.
Webinar: Functional Annotation and Analysis Strategies with OmicsBox and Blast2GO
Practical Approaches to the Functional Interpretation of Non-Model Organisms Datasets.
In this webinar you will learn:
-To functionally annotate sequence datasets using Blast2GO and OmicsBox.
-Explore downstream analysis options like enrichment analysis and pathway analysis.
-Practical demonstration using an RNA-Seq dataset from non-model organisms.
In this webinar, we will demonstrate how to functionally annotate any type of sequence dataset. The session will cover multiple annotation strategies with Blast2GO, ranging from maximum fidelity to high-coverage and permissive approaches.
Additionally, our team will show typical downstream analysis options, including enrichment analysis, pathway an...
In this webinar you will learn:
-To functionally annotate sequence datasets using Blast2GO and OmicsBox.
-Explore downstream analysis options like enrichment analysis and pathway analysis.
-Practical demonstration using an RNA-Seq dataset from non-model organisms.
In this webinar, we will demonstrate how to functionally annotate any type of sequence dataset. The session will cover multiple annotation strategies with Blast2GO, ranging from maximum fidelity to high-coverage and permissive approaches.
Additionally, our team will show typical downstream analysis options, including enrichment analysis, pathway an...
Просмотров: 235
Видео
OmicsBox Tips and Tricks
Просмотров 83Месяц назад
Welcome to our guide on maximizing your efficiency with OmicsBox! In this video, we explore the best tips and tricks that will help you get the full potential of our bioinformatics platform. Whether you're a beginner or an experienced user, you'll find some help to streamline your workflow and your analysis. How to... 0:13 - Run a Job 1:23 - Open Results 2:34 - Get Side Panels and Charts 3:11 -...
Webinar: Quantification and Functional Analysis of Long Reads
Просмотров 1142 месяца назад
Enjoy the first session of our webinar: Quantification and Functional Analysis of Long Reads in OmicsBox. In this webinar you will learn: -How to create high-quality transcript models from long reads. -Perform in-depth quality control and filtering with SQANTI3. -Carry out long-read quantification of non-model organisms. -Conduct a differential expression analysis and its functional interpretat...
Webinar: Definition and Curation of Long Read Transcriptomes
Просмотров 482 месяца назад
Enjoy the first session of our webinar: Definition and Curation of Long Read Transcriptomes with OmicsBox. In this webinar you will learn: -How to create high-quality transcript models from long reads. -Perform in-depth quality control and filtering with SQANTI3. -Carry out long-read quantification of non-model organisms. -Conduct a differential expression analysis and its functional interpreta...
Webinar: Trajectory Inference Analysis with Monocle3 in OmicsBox
Просмотров 1402 месяца назад
Enjoy the second session of our webinar "Exploratory Single-Cell RNA-Seq Analysis". This webinar will provide you with the essential tools and advanced techniques to transform raw data into meaningful biological insights. Perfect for bioinformaticians and researchers seeking to enhance their analysis capabilities, this session offers a comprehensive exploration of multi-sample scenarios and adv...
Webinar: Exploratory multi-sample Single-cell RNA-Seq analysis with OmicsBox
Просмотров 2552 месяца назад
Enjoy the first session of our webinar "Exploratory Single-Cell RNA-Seq Analysis". This webinar will provide you with the essential tools and advanced techniques to transform raw data into meaningful biological insights. Perfect for bioinformaticians and researchers seeking to enhance their analysis capabilities, this session offers a comprehensive exploration of multi-sample scenarios and adva...
Long-Read Isoform Identification and Quantification using IsoQuant
Просмотров 3,2 тыс.4 месяца назад
In this video tutorial, we will demonstrate how IsoQuant can be used to identify and quantify isoforms from long-read data in OmicsBox. LRGASP challenges: Systematic assessment of long-read RNA-seq methods for transcript identification and quantification | bioRxiv www.biorxiv.org/content/10.1101/2023.07.25.550582v1 IsoQuant repository: ablab/IsoQuant: Transcript discovery and quantification wit...
Gene Set Analysis of GWAS with Magma in OmicsBox
Просмотров 1,1 тыс.5 месяцев назад
0:00 - Introduction 2:22 - GWAS Analysis in OmicsBox | Setting the Parameters 4:24 - Analyzing the output 6:00 - MAGMA Analysis in OmicsBox | Setting the Parameters 7:53 Analyzing the output 9:55 - Conclusions Download OmicsBox for Free: www.biobam.com/trial/
Quality Assessment and comparison of de novo genome assemblies using QUAST
Просмотров 4,1 тыс.6 месяцев назад
In this video tutorial, we will show how QUAST can be used to compare and assess the quality of different assembly strategies using OmicsBox. 0:00 - Intro 0:20 - Why Compare de novo assemblies 1:44 - OmicsBox Tutorial 1:59 - Run DNA-Seq de novo Assembly 2:15 - Run QUAST 3:46 - QUAST Output 4:25 - Comparing Assemblies' Length and Fragmentation 6:16 - Comparing Assemblies' Contiguity 8:56 - Compa...
OmicsBox: The All-In-One Bioinformatics Software
Просмотров 49 тыс.Год назад
Download NOW! the most powerfull and user-friendly bioinformatics software. 👉 www.biobam.com/trial/ #OmicsBox is a leading bioinformatics solution that offers end-to-end NGS data analysis of genomes, transcriptomes, and metagenomes. The application is used by top private and public research institutions worldwide and allows researchers to easily process large and complex data sets, and streamli...
Single-Cell RNA-Seq Clustering with OmicsBox 2.2
Просмотров 7 тыс.Год назад
🧬 Single-Cell Rna-Seq Clustering is a feature included in the Transcriptomics Module: www.biobam.com/transcriptomics/ 🔗 All new features and improvements of OmicsBox 2.2 can be found in our blog: www.biobam.com/omicsbox-2-2-release/ OmicsBox is the All-in-One bioinformatics software solution for your omics data analysis. From raw read to functional insights. Fast and easy!
Long Read Quality Assessment with LongQC
Просмотров 4,6 тыс.Год назад
🧬 LongQC is a bioinformatic tool that allows the quality control of long reads data from major TGS technologies. It provides useful statistics and charts to evaluate the quality of any dataset efficiently. Learn more in our blog: www.biobam.com/longqc-reads-quality-assessment/ 🔗LongQC is included in the General Tools Module of OmicsBox 2.2 along with some other quality control and preprocessing...
Transcriptome Analysis with SQANTI3 in OmicsBox 2.2
Просмотров 335Год назад
🧬 SQANTI3 is now available in OmicsBox 2.2 Transcriptomics Module. Learn more about this new feature in our blog: www.biobam.com/transcriptome-analysis-with-sqanti3/ 🔗 All new features and improvements of OmicsBox 2.2 can be found in our blog: www.biobam.com/omicsbox-2-2-release/ OmicsBox is the All-in-One bioinformatics software solution for your omics data analysis. From raw read to functiona...
scRNA-Seq Trajectory Interference with Monocle 3
Просмотров 56 тыс.Год назад
🧬 Monocle is a tool to analyze Single Cell RNA-Seq data to calculate cell trajectories and track changes over time. These tools can be found in the Transcriptomics Module under Trajectory Inference in OmicsBox 2.2: www.biobam.com/omicsbox/ 🔗 All new improvements of OmicsBox 2.2 can be found in our blog: www.biobam.com/omicsbox-2-2-release/ OmicsBox is the All-in-One bioinformatics software solu...
Single-Cell RNA-Seq Differential Expression Analysis with OmicsBox 2.2
Просмотров 311Год назад
🧬Single-Cell RNA-Seq Differential Expression Analysis is a new feature of OmicsBox 2.2: www.biobam.com/omicsbox/ 🔗 All new improvements of OmicsBox 2.2 can be found in our blog: www.biobam.com/omicsbox-2-2-release/ OmicsBox is the All-in-One bioinformatics software solution for your omics data analysis. From raw read to functional insights. Fast and easy!
How to use the MLST App in Omicsbox
Просмотров 2,9 тыс.5 лет назад
How to use the MLST App in Omicsbox
How to use "Retrieve Blast Top-Hit" with OmicsBox/Blast2GO
Просмотров 1,6 тыс.5 лет назад
How to use "Retrieve Blast Top-Hit" with OmicsBox/Blast2GO
RNA-Seq Features in OmicsBox/Blast2GO
Просмотров 1,8 тыс.5 лет назад
RNA-Seq Features in OmicsBox/Blast2GO
Webinar: De-Novo Transcriptome Analysis the Cactus Root Development with OmicsBox/Blast2GO
Просмотров 1,3 тыс.6 лет назад
Webinar: De-Novo Transcriptome Analysis the Cactus Root Development with OmicsBox/Blast2GO
How to create Workflows with OmicsBox/Blast2GO
Просмотров 4,3 тыс.6 лет назад
How to create Workflows with OmicsBox/Blast2GO
Estimating Transcript-Level Expression with Blast2GO
Просмотров 1,7 тыс.6 лет назад
Estimating Transcript-Level Expression with Blast2GO
Coding Potential Assesement Tool with Blast2GO
Просмотров 6617 лет назад
Coding Potential Assesement Tool with Blast2GO
NCBI GenBank Submission with Blast2GO
Просмотров 3,5 тыс.7 лет назад
NCBI GenBank Submission with Blast2GO
Time Course Expression Analysis with Blast2GO
Просмотров 2,9 тыс.7 лет назад
Time Course Expression Analysis with Blast2GO
Pairwise differential expression analysis with Blast2GO
Просмотров 4,2 тыс.7 лет назад
Pairwise differential expression analysis with Blast2GO
How to translate longest ORFs with Blast2GO
Просмотров 5957 лет назад
How to translate longest ORFs with Blast2GO
How to perform Gene Set Enrichment Analysis (GSEA) with OmicsBox/Blast2GO
Просмотров 34 тыс.8 лет назад
How to perform Gene Set Enrichment Analysis (GSEA) with OmicsBox/Blast2GO
Hey can you please give detail video in gsea
Kindly let us know that whwre is the analysis and GSEA option in omits tool I have just take a trial o omits 3.9.3 Not find Gsea option???
Great Work! Also IsoQuant has just been mentioned as one of the most effective tool by a Nature Communication: DOI: 10.1038/s41467-024-48117-3
Good job! Very interesting :)
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😊
Does this video not have sound?
Hello Lindsey! This specific video has no audio, sorry for any inconvenience.
Do you mind sharing information regarding the .FASTA file that you got out of nowhere as I have a .gz file and extraction results in a large number of other files. So could you tell tell us how did you manage to get a FASTA file?
how to create a fasta file of all my proteins?
question... why is this function removed in the 6.0.1 version?
What does GO mean
Gene Ontology
Hi! Do the id's from the test set have to be in a specific order to do this test?? For example, from the biggest Log2FC value to the smallest value?
Thank you. why the video doesn't have any sounds?
Are all of the samples TMM normalized together, or are they TMM normalized within each experimental group/condition/timepoint?
very informative
Hi! You have a .gz file but the "make a blast database" accepts fasta files. How can you convert it?
Hi! I have a question: How can I do a spreadsheet from two archives .fastq? Thanks!!
I'm running a transcriptome study and my seq name columns is populated by the codes of my contgis, it's possible to run this analysis around the content of description column (which contaisn my uniprot accesion codes obtained after blastx)?? or it's mandatory to modify the seqname column to contain these codes wich I have mentioned and then perfom the test??
It is important that the names of your ID lists (test and/or reference set) are the same as the sequence name column of you annotated blast2go project. If the Id list you have are the values which appear in the description column you could use the "select by description function" in combination with the "Create ID list of Column" context menu to create the "translated" ID lists. Maybe this video might also be helpful since it shows how to create ID list from a selection: ruclips.net/video/MWMTcgq-wEY/видео.html
HI, Thanks for this video. Where can I download biomart_data_mmusculus_gene_entrez file?
How do you switch the view t 0:30?
Hi. In t 0:30 the video switches to a spreadsheet like Excel, not to a view within Blast2GO.
But where do I get my Ensembl IDs when I have a B2G File that ist already processed (Blast- Interpro-Mapping-Annot)?
In this case, we obtained the GO annotated human genes with Ensembl IDs via BioMart as reference, so we use the Ensembl IDs as test set (see ruclips.net/video/HP4JfENFFPs/видео.html). If you already have an annotated data set just make sure that your test set IDs used for the Fisher's Exact Test have the same IDs as your Blast2GO project.