Bioinformatics.ca is dedicated to creating and maintaining a skilled bioinformatics workforce through open content. Our workshops are recorded and posted here and our materials can be found at bioinformaticsdotca.github.io.
If you are interested in attending a workshop, you can find our current schedule at bioinformatics.ca/.
This is the RU-vid channel for the Canadian Bioinformatics Workshops. The workshops are offered every year online and across Canada; lecture recordings are posted here and course materials are posted at our student website (linked in video descriptions).
Hi thank you for this valuable workshop. I would like to ask if the functional analysis for untarget metabolomics can also be applied for NMR data? Thank you.
Good comprehensive video. One comment regarding differential expression analysis post-integration (starting at 56:27). In either bulk or single-cell sequencing, most tools highly recommend NOT doing DE analysis on corrected data, exactly because of the concerns regarding under- or over-correction and removing potential biological variation. If you read the literature around older batch correction tools such as ComBat, most recommend that DE analysis correct for batch effects within the statistical model (i.e. including a model of ~ Batch + Condition). Obviously, Seurat doesn't have that functionality, but if you perform pseudobulk aggregation for DE analysis (literature suggests this is more statistically sound), then tools capable of including batch effects in the regression model (DESeq2, edgeR, limma-voom, etc.) are available.
Hello thank you for the lecture. I would like to ask which metabolite set library I should use for enrichment analysis if I am doing human cell extract metabolomics? Thank you.
Can you please upload a tutorial on EnrichmentMap with GSEA data results and network analysis? And how to generate a heat map from the GSEA data pathways. I would really appreciate it. Great tutorial on this one.
Intro to R only had two lectures (module 1 and module 4); the remaining material was taught through code-along R Markdown files. You can find them at the course material link in the description. Hope this helps!
Hi, I have some questions regarding this. I am trying to make my own network. I have got 1000 gene IDs which are sorted in 6 clusters. All ID's contain descriptive information about the gene, and have got relative expressions for 8 different times (healthy vs sick). I have got all this data, but do not know how to import it in the right way into cytoscape. Could you help me with this? With kind regards, Jip
I suggest you contact the instructor directly and ask her: Lauren Erdman <larunerdman1@gmail.com>. Get back to us if you don't get an answer. (course_info@bioinformatics.ca)
Just a warning message so should be fine to proceed. Errors and warnings are distinct in R and warnings are just there to let you know some important information.
Hi! Thank you for making these resources openly available. I am following this series/workshop by myself (I was not registrant) and I feel this section should follow (as in go after) the section in the "CBW’s INtroduction to R workshop - 02: Your second script" video.
@@FrancisOuellette_bffo On the video, so people can move through the workshop and skips parts and go to bits they need to learn or relearn. E.g. 59:26 Starts Creating Factors. Do you get what I mean ?
@@alialijama9098 Yes, I do -- I have not done that, but it is an excellent idea ... I will consider ... In my (absent) free time ... But yes, it would be a great addition. Maybe for a summer student. Those timestamps seem to be a lot of work. Are there video tools to help with that? (let me search -- but be free to point) -- Just found this: ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-FOMWgFlmo-8.html ... Will look into it further. Thank you for the suggestion -- great idea!
@@FrancisOuellette_bffo I am pretty sure there are, I have seen Freecodecamp use them all the time. Lots of them, see below. You're welcome. I would believe there should be an easier way than getting someone else to do it. ru-vid.com?search_query=how+to+create+timestamps+on+youtube
