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BioBam Bioinformatics
Spain
Registrace 4. 11. 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: Quantification and Functional Analysis of Long Reads
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 interpretation
This webinar covers the main analysis steps of long-read RNA-Seq analysis. We will focus on Transcript Identification using reference-guided tools like FLAIR or IsoQuant. Next, we cover transcriptome quality control and filtering, followed by quantification and differential expression analysis.
Using real data and practical examples, our team will demonstrate the comprehensive long-read RNA-Seq analysis features available in OmicsBox. OmicsBox simplifies the use of tools such as FLAIR, IsoQuant, and SQANTI3, allowing us to convert raw reads into transcripts to gain important perspectives.
Interested in getting your genomic research to the next level?
Book a custom OmicsBox Demo with our bioinformatics team: www.biobam.com/book-a-demo/
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 interpretation
This webinar covers the main analysis steps of long-read RNA-Seq analysis. We will focus on Transcript Identification using reference-guided tools like FLAIR or IsoQuant. Next, we cover transcriptome quality control and filtering, followed by quantification and differential expression analysis.
Using real data and practical examples, our team will demonstrate the comprehensive long-read RNA-Seq analysis features available in OmicsBox. OmicsBox simplifies the use of tools such as FLAIR, IsoQuant, and SQANTI3, allowing us to convert raw reads into transcripts to gain important perspectives.
Interested in getting your genomic research to the next level?
Book a custom OmicsBox Demo with our bioinformatics team: www.biobam.com/book-a-demo/
zhlédnutí: 16
Video
Webinar: Definition and Curation of Long Read Transcriptomes
zhlédnutí 9Před 2 hodinami
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
zhlédnutí 77Před 21 dnem
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
zhlédnutí 115Před 21 dnem
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
zhlédnutí 1,5KPřed měsícem
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
zhlédnutí 985Před 3 měsíci
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
zhlédnutí 4KPřed 3 měsíci
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
zhlédnutí 49KPřed rokem
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
zhlédnutí 7KPřed rokem
🧬 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
zhlédnutí 4,5KPřed rokem
🧬 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
zhlédnutí 303Před rokem
🧬 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
zhlédnutí 56KPřed rokem
🧬 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
zhlédnutí 288Před rokem
🧬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
zhlédnutí 2,9KPřed 4 lety
This video introduce the OmicsBox App which allows you to perform Multi-Locus Sequence Typing (MLST) analysis fast and easy in multiple files at the same time… Bioinformatics made easy!
OmicsBox Presentation
zhlédnutí 8KPřed 5 lety
OmicsBox is a bioinformatics software for the analysis of NGS data. This video shows the main features included in each module: functional analysis, transcriptomics, metagenomics and genome analysis. www.biobam.com/omicsbox
How to use "Retrieve Blast Top-Hit" with OmicsBox/Blast2GO
zhlédnutí 1,6KPřed 5 lety
How to use "Retrieve Blast Top-Hit" with OmicsBox/Blast2GO
Webinar: De-Novo Transcriptome Analysis the Cactus Root Development with OmicsBox/Blast2GO
zhlédnutí 1,2KPřed 6 lety
Webinar: De-Novo Transcriptome Analysis the Cactus Root Development with OmicsBox/Blast2GO
How to create Workflows with OmicsBox/Blast2GO
zhlédnutí 4,2KPřed 6 lety
How to create Workflows with OmicsBox/Blast2GO
Estimating Transcript-Level Expression with Blast2GO
zhlédnutí 1,6KPřed 6 lety
Estimating Transcript-Level Expression with Blast2GO
Coding Potential Assesement Tool with Blast2GO
zhlédnutí 650Před 7 lety
Coding Potential Assesement Tool with Blast2GO
Time Course Expression Analysis with Blast2GO
zhlédnutí 2,8KPřed 7 lety
Time Course Expression Analysis with Blast2GO
Pairwise differential expression analysis with Blast2GO
zhlédnutí 4,2KPřed 7 lety
Pairwise differential expression analysis with Blast2GO
How to translate longest ORFs with Blast2GO
zhlédnutí 592Před 7 lety
How to translate longest ORFs with Blast2GO
How to perform Gene Set Enrichment Analysis (GSEA) with OmicsBox/Blast2GO
zhlédnutí 34KPřed 7 lety
How to perform Gene Set Enrichment Analysis (GSEA) with OmicsBox/Blast2GO
Coloured Graphs: How to combine multiple functional GO profiles with Blast2GO
zhlédnutí 914Před 7 lety
Coloured Graphs: How to combine multiple functional GO profiles with Blast2GO
How to select sequences by function and create ID lists with Blast2GO
zhlédnutí 2KPřed 7 lety
How to select sequences by function and create ID lists with 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: czcams.com/video/MWMTcgq-wEY/video.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 czcams.com/video/HP4JfENFFPs/video.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.