Single-cell trajectory and pseudotime analysis with Monocle3 and Seurat in R

[@luzhang5100]

Hi @Sanbomics Thank you for your video.I wonder if is possible to use Scanpy Generated UMAP for Monocle3 trajectory analysis? it seems no suitable way in the internet.

[@sanbomics]

If you transfer your data from scanpy to seurat and include your UMAP reduction and coordinates you can probably do it. Alternatively, you can take a look at my most recent video which covers psuedotime in python on a scanpy object

[@luzhang5100]

@@sanbomics Thank you for your reply. As you said, I have completed the analysis of monocle. Thank you. And i also noticed that your most recent video for CellOracle! seems great!

[@hiepnguyen7343]

Great job. Thank you

[@marymmostafa8740]

I was implementing the code and was wondering what is the cds_pt_res.rds written in cds_pt_res

[@sanbomics]

Oh, I might have just left that in there on accident. I was just saving the output to file so I didn't have to run the command again.

[@sajtoslaszlo5287]

I loaded all package but this rasterizeBy function is not found. What package is this function in? Thanks in advance

[@sanbomics]

Thats unfortunate. I am not sure off the top of my head. Were you able to figure it out?

[@mujahidsourav5379]

Thank's for your work❤️..i'm tryinh to install monocle3 and seurat-wrappers on R 4.3.2.using devtools and remotes..bt failed.. What should i do?

[@SoyKhalid]

Hey there, I hope that this helps. I ended up using Seurat v 2.3.4 in order to get Seurat wrappers to work with my existing dataset.

[@BharatiMehani]

Hi @Sanbomics Thank you for your video. I tried to ran these commands on my dataset but at line 140 and with command: plot_cells(cds,show_trajectory_graph=F,color_cells_by="partition"), I am getting an error: Error: Must request at least one colour from a hue palette. Can you please guide what am I missing and how can I troubleshoot this error?

[@sanbomics]

Hmm that is weird I haven't seen that before. Have you figured it out? Sorry for late reply

[@yarazidan3931]

Can i ask you which version of RStudio are working on? and also what other platforms can we use instead of it?

[@pietrocestola7856]

It's not clear to me how the pseudotimes are calculated since not all points in the dataset belong to the tree. Geodetic distance is usable if all points belong to the tree, so how are pseudotimes actually calculated?

[@sanbomics]

Each cell is projected onto the closest point on the trajectory to calculate pseudotime regardless of where the cell originally is in the reduced dimensional space. This is how it is calculated for all the cells even if they don't sit on the trajectory.

[@jianhuacao7180]

Hi, dude, what's the key differences between this trajectory and the velocity you told before?

[@sanbomics]

Trajectory is a function of the gene expression change over time: "The gene expression of this cell is most similar with this cell". Velocity accounts for the proportion of nascent and mature RNA. The latter is a little more sophisticated imo, but they both have pros/cons

[@BayAreaLakers]

If you have the known time, then is it even necessary to look at differential expression across pseudotime? Isn't it more biologically relevant to look at differential expression along actual time?

[@sanbomics]

Yes, but you don't usually have the known time. This was just a nice way to compare the two

[@BayAreaLakers]

@@sanbomics Thanks!

[@marwanmohamed6575]

Great job thank you alot, would it be possible to do a tutorial For SCENIC (Single-Cell Regulatory Network Inference) Or if you know any alternatives for Regulons inference would be very helpfull. thanks alot again your vidios are helping tons of Junior bioinformaticion all over the world.

[@sanbomics]

Hi! I have thought of doing a SCENIC one. I do cover BITFAM which is a TF activity inference tool

[@marwanmohamed6575]

@@sanbomics thanks alot, doing scenic will be super amazing and useful

[@researchonfungi3232]

Hi,I am bioinformatics biggner and your video is very informative and easy to follow.I want to generate RNA editing event data from raw RNAseq data .Could you please make a vedio on RNA editing Or can you make a playlist which we can follow step by step? Because I did not find any video in youtube which I can follow step by step .Thanks in advance🙏🙏🙏

[@sanbomics]

Hi, sure! exactly what do you mean by RNA editing? Splicing events / isoforms?