Introduction to single-cell RNA-Seq and Seurat | Bioinformatics for beginners

[@rohitsatyam2935]

Single Cell Analysis has been a lonely world for me so far. Happy to find someone is putting up efforts to make it easier for starters!!

[@kitdordkhar4964]

I am a biologist learning scRNAseq from scratch. So I am glad to see your tutorial. Adding yours to the list of mentors! Please provide more details on how to analyze multiple 10x samples or replicates. The seurat vignette had the merge() function but I am not sure how to apply split.by comparing the features. Cheers for your channel!

[@Bioinformagician]

Hi, thank you for your kind words, I am glad you find my channel helpful! My next video is about merging and integrating scRNA-Seq datasets, I am still working on it. Hopefully it answers all your questions. Stay tuned! :)

[@rohitsatyam2935]

@@Bioinformagician Also, if you can shed some light on how to combine replicates in Seurat in a control-case experiment (3 control replicates, 3 treatment replicates).

[@Bioinformagician]

​@@rohitsatyam2935 Are the replicates in each condition, biological or technical? Also, do you see batch effects within your replicates?

[@ahmedrizk59]

I am currently studying stat115 and i want to learn single cell,can you please share the goog resources you found

[@NishantSharma-f8b]

Commendable. Thanks for uploading this useful video.

[@sakichan2640]

Thank you sister. I hope there will be more pratical projects soon

[@fgfanta]

Let's gooooo!

[@francis2836]

Well what can I say, just perfect Thank you :)

[@tushardhyani3931]

Thank you for this video !!

[@pksPyaariZindagi]

You explained it very well! 👍

[@animatedbiologywitharpan]

Can you make a video on pseudo time analysis from single cell data?

[@Bioinformagician]

Sure, it is definitely in the pipeline. Will be soon posting a video on it! Thank you for the suggestion :)

[@michelleyibingwei9400]

Request to review Giotto for spatial transcriptomic analysis. Your videos have been very helpful

[@Bioinformagician]

I will check it out. Thanks!

[@takeonme7477]

Very helpful thank you so much!

[@kshajby6839]

thanks so much for this

[@chrisdoan3210]

Thank you for a helpful video! I could not find the video you mentioned in the basic terminologies part of this video. Would you please tell me where I can find it?

[@Bioinformagician]

Here's the link to the video - kzbin.info/www/bejne/aIOpin6Kq6iLftU

[@sheikhmujibur4890]

Mam can you please explain more about UMI and how to apply and tools

[@nandinipatel4349]

Hi Khushbu, this video was really helpful and when I tried the integration tutorial, my R ran into vector exhaustion error and then the R session quit and my MacBook kinda crashed..so I wanted to ask you that which MacBook do you use ? Do you think it’s a RAM issue cuz I’m using 8gb RAM MacBook !

[@hafeezuom1422]

Dear Khushbu, your method of teaching is really superb. Guide me please in creating Seurat object of SCRNA Seq data of ArrayExpress like E-MTAB-7704. Thanking you in anticipation

[@Bioinformagician]

Did you try downloading and looking at the processed files?

[@hafeezuom1422]

@@Bioinformagician yes I did. It's a txt file. Actually I am following your videos in which you told about 5 different formats for creating Seurat object. I don't know how to create Seurat object from txt file or CSV file.

[@hafeezuom1422]

I m searching for any R script to work with preprocessed data like ArrayExpress

[@hafeezuom1422]

@@Bioinformagician Dear Khushbu, it is to inform you that the issue is resolved Alhamdolillah. I converted the text file first to Market matrix format. Then I created the seurat object from it. Its working now. I am applying your code of analyzing scRNA data.

[@Bioinformagician]

@@hafeezuom1422 That's amazing!👏

[@stretch8390]

Are you a Seurat advocate or package agnostic when it comes to single cell workflows in R? I'm just venturing into them now and this video is very helpful thanks.

[@Bioinformagician]

I am package agnostic. I prefer Seurat but I think there are many other packages that can achieve what Seurat can. Explore them all and decide which one works best for you.

[@gunanadar5401]

Hello Khushbu, I'm a beginner in R language and i want to create tSNE plot for single cell RNAseq data for embroids. Like stages of embryos and my gene of interest So I'm finding different to create dataset and idk what all information is required Can you please help me asap ? Plzz

[@LanaDominkovic]

Do you know about a tool for bulk rna seq in python? I am aware about scanpy for single cell rna seq but not for bulk. Very good video, thanks!

[@Bioinformagician]

Thank you for your comment, since I do not actively work in python, my knowledge about python packages and tools to process bulk RNA-seq data is limited. However, I am sure there are several python packages to do similar things with the bulk data. Are you looking for a specific analysis for bulk RNA-seq?

[@LanaDominkovic]

@@Bioinformagician I tried to find some because I wanted to do some bulk rna seq but I could not find anything for python. also additional question, do you know where can I download scrna seq datasets? I think your previous video was only bulk rna seq if I am not mistaken? sry if question is stupid, but I am newbie in this field :D

[@Bioinformagician]

@@LanaDominkovic No question is stupid :) You can find a lot of scRNA-seq datasets on NCBI GEO. One of my go to places for scRNA is 10X website (www.10xgenomics.com/resources/datasets). Also, there are tons of papers generating single cell data, those are the rich sources to get your hands on such datasets and start playing with it. Hope this helps!

[@msumode4493]

I was wondering how to make an assay within Seurat using metadata information. Would you please be able to share some pointers or a script I could repurpose? Thanks.

[@Bioinformagician]

Assay in Seurat is meant to store multiple 'transformations' of the data, including raw counts (@counts slot), normalized data (@data slot), and scaled data for dimensional reduction (@scale.data slot) and not the metadata. Check this out - github.com/satijalab/seurat/wiki/Assay

[@alson9384]

Nothing but