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Cellenics Showcase - Shared screen with speaker view
Evanna Mills
18:50
zero experience
Rachel Battaglia
18:51
Total beginner!
Majd Al Suqri
18:52
No experience
accalia fu
18:55
no experience
Rinaldo Catta-Preta
18:56
somewhat experienced
Jacob Haase
18:56
little bit
Mahtab Dastpak
19:02
Little bit
Laura Bricio Moreno
19:02
No experience
Matthew Torre
19:04
No prior experience
Ayano Kohlgruber
19:04
some R-based analysis
chih-hao wang
19:07
No experience
Vanitha Nithianandam
19:12
Starting
joseph Bonventre
19:12
very little
Olivier Pourqiue
19:14
Little bit
Farnaz Shamsi
19:15
Somewhat experienced
Sudhir Gopal
19:16
A little
Ah-Ram Kim
19:20
Very little
Rachel Battaglia
19:21
yes
Laura Bricio Moreno
19:22
yes
Hassan Bukhari
19:23
A little
Rinaldo Catta-Preta
19:23
no
Evanna Mills
19:25
yes
Ayano Kohlgruber
19:32
yes
Vanitha Nithianandam
19:34
yes
Mahtab Dastpak
19:36
I’m interested to learn to design my experiments
Farnaz Shamsi
19:38
Yes
accalia fu
19:40
yes my own data set, n=1 so far with 3 samples
gabriela venturini da silva
19:46
yes
Matthew Torre
19:48
not yet
joseph Bonventre
19:52
yes, my own
Hassan Bukhari
19:52
Yes
Preetida Bhetariya
19:56
yes
Ah-Ram Kim
19:56
yes
Ying Liu
19:56
Yes, my own
Kemar Brown
19:59
Yes and Yes
Jacob Haase
19:59
yes
Olivier Pourqiue
20:07
Yes
William Hou
28:55
Thank you, I have some Seurat based analysis of 10X data, but have difficults for the scRNA-seq integration (joint analysis of two or more single-cell datasets) and reduction of the batch effect.
Rinaldo Catta-Preta
29:46
will the recording be made available?
Alex Pickering
30:01
Yes we will send out a link once it's up :)
Alex Pickering
31:10
Great to hear William, Oliver will cover dataset integration when he introduces the Data Processing module so stay tuned
William Hou
31:45
Thank you, Alex.
Oliver Gibson - Biomage
34:47
Welcome to the Single Cell RNA-seq Analysis WorkshopCellenics Single Cell RNA-seq Analysis Platform link:https://scp.biomage.net/
Book a meeting to discuss your analysis:https://calendly.com/alexpickering/cellenics
Slides and exercises:https://drive.google.com/file/d/16WhdcNDvP3wdApII89qGKG5qArPAUdM2/view
Rinaldo Catta-Preta
35:02
will that work in Safari?
accalia fu
35:08
chrome
Evanna Mills
35:21
in
Farnaz Shamsi
35:21
I’m in!
Shi Fang
35:23
in
Jacob Haase
35:23
I'm in
gabriela venturini da silva
35:24
I'm in
Laura Bricio Moreno
35:25
Does it have to be chrome, or can it be safari?
Ah-Ram Kim
35:25
in
Wonseok Lee
35:26
I’m in
Majd Al Suqri
35:28
I’m in
Marianna Zazhytska
35:28
in
Zhe Li
35:37
in
Jessica Garbern
35:41
in
Vanitha Nithianandam
35:42
in
Olivier Pourqiue
35:49
I have not received login instruction
Baolong Xia
35:55
in
Laura Bricio Moreno
35:56
Ok, thank you!
Annie Hsieh
35:58
I am in
Rinaldo Catta-Preta
36:01
thanks
Rachel Battaglia
36:01
in
Matthew Torre
36:10
I'm in
Hassan Bukhari
36:12
in
Laura Bricio Moreno
36:28
I am in
Ying Liu
36:38
in
Sudhir Gopal
36:42
https://harvard.zoom.us/w/98146373411?tk=eWzDcWvJjVv3SdlOBQWyYoHt6FXyzR-cMwlY4K35838.DQMAAAAW2frPIxZoV09MMXh3QVFMYUVjbDJpbjg5UjlRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA&pwd=OHFqQklPbUJZVWxXaHRyWEdNSUlTZz09
Mahtab Dastpak
36:42
in
Sudhir Gopal
36:57
sorry, I also did not receive
David Hill
38:22
In
Oliver Gibson - Biomage
38:25
Cellenics Single Cell RNA-seq Analysis Platform link:https://scp.biomage.net/
Book a meeting to discuss your analysis:https://calendly.com/alexpickering/cellenics
Slides and exercises:https://drive.google.com/file/d/16WhdcNDvP3wdApII89qGKG5qArPAUdM2/view
joseph Bonventre
38:46
I cannot get in
accalia fu
41:24
Hi, Q please, What are the formats that you upload? raw file? H5?
Jacob Haase
41:50
How long does the processing of a full dataset take in average on cellenics?
Oliver Gibson - Biomage
42:01
We will address data types in detail near the end of the workshop, but we support the raw barcodes/features/atrix files, standard output from cellranger
accalia fu
42:14
ok thanks
Alex Pickering
43:38
Hi Jacob, processing time varies a lot with the project. Depends on number of samples, cells in a sample, integration method etc. Can be as little as a few minutes or quite a bit longer
Jacob Haase
47:02
Okay thank you. This means cellenics has a massive number of processing cores and memory in the background?
gabriela venturini da silva
47:48
Is there any pre set for single nucseq thresholds?
Alex Pickering
50:55
Hi Gabriela, no there are not any different presets for snRNAseq. That being said the filters can all be adjusted to suit
Mahtab Dastpak
51:52
The last one is Umap results, right?
Mahtab Dastpak
52:02
The clustering the data
Mahtab Dastpak
52:22
If, yes, I am done
Farnaz Shamsi
52:26
Done1
gabriela venturini da silva
52:31
done
Marianna Zazhytska
52:32
Done1
Jacob Haase
52:38
done
Ying Liu
52:44
Done 1
Laura Bricio Moreno
52:45
done
Annie Hsieh
52:46
Done
Rachel Battaglia
52:48
done
Olivier Pourqiue
52:49
Done
Evanna Mills
52:50
1
Shi Fang
52:51
Done
Ah-Ram Kim
52:52
done1
Vicky Morrison - Biomage
53:07
Hi Gabriela. We have several users who have analysed snRNA-seq data in Cellenics - our default pipeline works well with this data type. The one filter where particular attention should be paid is the mitochondrial content filter. You might consider disabling this filter.
David Hill
53:19
done 1
Ayano Kohlgruber
53:28
done 1
Vanitha Nithianandam
53:28
done 1
Matthew Torre
53:32
Done 1
Kemar Brown
53:44
done 1
Sudhir Gopal
53:46
done1
gabriela venturini da silva
53:47
Thank you!
gabriela venturini da silva
54:09
the Plot styling function is not working, right?
Hassan Bukhari
54:18
Done 1.
Zhe Li
54:18
done 1
Shi Fang
54:18
second sample looks really different in the filters. Can it be due to a biological differences? i.e. what if one group is more prone to cell death. How is that going to change the filter threshold?
Kemar Brown
54:29
Sorry I missed this. Are we using both solo and scrublet to detect doublets?
William Hou
54:33
done1
Alex Pickering
54:42
scDblFinder
Alex Pickering
54:48
for doublets*
joseph Bonventre
54:51
done 1
Rinaldo Catta-Preta
55:11
done
Wonseok Lee
55:29
done
Martin Fosco - Biomage
55:37
Jacob Haase: the backend we use to process has 28Gb of ram
William Hou
01:00:27
I see we have several intergartion methods, what is the diffeent?
Ayano Kohlgruber
01:01:35
i noticed that in data processing step 4, there was a cluster in all 3 datasets that deviated from the rest. if we wanted to include that lower cluster and then look to see what changes occur in the UMAP, how might we do this?
Oliver Gibson - Biomage
01:02:12
Ayano, that’s a great question!
Oliver Gibson - Biomage
01:02:32
I’ll try to answer it out loud as soon as vicky’s done presenting the data exploration module
Ayano Kohlgruber
01:04:00
great, thank you!
Oliver Gibson - Biomage
01:04:21
We actually used to have an exercise for this in the workshop before
Oliver Gibson - Biomage
01:04:49
It’s an interesting question in this particular dataset, if you are curious after the workshop you should definitely take a look.
Laura Bricio Moreno
01:08:33
Does the program only detect PMBCs, or would it also classify other cell types, such as neurons, microglia, etc?
Oliver Gibson - Biomage
01:09:22
We don’t currently have automatic cluster annotation to actually annotate the cell types. It’s a feature we really want to have and are working on getting in the platform.
Mahtab Dastpak
01:09:29
I just received this email: “The data processing pipeline has completed successfully and your data is now ready to explore”. What is mean?
Oliver Gibson - Biomage
01:10:12
That being said, the clustering method can work with any cell types, it will just cluster cells together based on similarity leading to the grouping into cell types
Oliver Gibson - Biomage
01:10:33
Then the user will need to -using biological knowledge of the data- identify those cell types
William Hou
01:11:33
Hello Mahtab, I think you need to use the marker gene to identify the cell type
Laura Bricio Moreno
01:14:13
My clusters look different, clusters 3,4 and 8 look the same, but the rest are kind of upside down. Is that normal>
Farnaz Shamsi
01:15:12
Done2
Laura Bricio Moreno
01:15:56
Great, thanks!
Jacob Haase
01:16:06
done 2
Vicky Morrison - Biomage
01:16:11
Hi Mahtab. When the data processing pipeline runs, it sends you an email to inform you when the pipeline completes successfully. (You can opt out.) This allows you to go away and work on something else whilst your pipeline is running! So it sounds like you have received this email because your pipeline re-ran. This could have been you in the workshop or it could have been before the workshop when we uploaded the dataset to your account.
joseph Bonventre
01:16:49
In step 3 please explain what you mean by “relevant genes?”
Annie Hsieh
01:17:46
Done 2
gabriela venturini da silva
01:17:52
done 2
Rachel Battaglia
01:17:55
Done 2
Ying Liu
01:18:00
Done 2
Ayano Kohlgruber
01:18:06
Done 2
Evanna Mills
01:18:10
done 2
Mahtab Dastpak
01:18:13
I could check the genes. But I missed how to annotate the cluster types.
Mahtab Dastpak
01:18:17
Done 2
Sudhir Gopal
01:18:28
Done 2
Farnaz Shamsi
01:18:45
Is there any way to select a custom cell set based on the expression of a gene/set of genes?
Olivier Pourqiue
01:19:17
Done 2
Zhe Li
01:19:21
Done 2
Hassan Bukhari
01:19:29
Done 2
Marianna Zazhytska
01:20:12
Done2
Rinaldo Catta-Preta
01:20:50
Done 2
gabriela venturini da silva
01:20:52
Can I isolate the cells in a cluster and run a new clustering with only this subset of cells?
Matthew Torre
01:20:59
Done 2
Vanitha Nithianandam
01:21:34
Done 2
gabriela venturini da silva
01:21:37
thank you
Farnaz Shamsi
01:22:25
Can Cellenics be used to analyze data from CITE-seq or other multiplexing methods?
Oliver Gibson - Biomage
01:23:44
Farnaz, we currently don’t support CITE-seq data. If you upload rna-seq + CITE-seq data to Cellenics the CITE assay will be ignored, but you will still be able to analyse your RNA-seq data.
Oliver Gibson - Biomage
01:23:59
We do want to implement this feature, and it’s high in our priority list!
Farnaz Shamsi
01:24:26
Thank you
Vicky Morrison - Biomage
01:25:02
Great suggestion Farnaz - thanks for suggesting this feature! It helps us to prioritise what features we build next!
Ah-Ram Kim
01:25:45
Can I upload and use custom reference?
Mahtab Dastpak
01:26:50
Can the Cellenics support mRNA splicing process for detection the mis-spliced patterns?
William Hou
01:27:52
Can cellenics be used to analyze the zebrafish sincle cell RNA-Seq data?
Ayano Kohlgruber
01:28:47
Done 3
Rachel Battaglia
01:28:50
Done 3
Evanna Mills
01:28:58
done 3
Jacob Haase
01:29:20
done 3
William Hou
01:29:33
Thank you, Alex.
gabriela venturini da silva
01:29:35
done 3
Marianna Zazhytska
01:29:52
done3
Majd Al Suqri
01:30:03
Done 3
Matthew Torre
01:30:09
Done 3
Sudhir Gopal
01:30:12
Done 3
Annie Hsieh
01:30:16
Done 3
Ah-Ram Kim
01:30:32
Done 3
Ying Liu
01:30:37
Done 3
Zhe Li
01:30:39
Done 3
Laura Bricio Moreno
01:30:43
done
Annie Hsieh
01:30:55
Can Cellenics compare two different single cell sequencing data from two different publications?
Farnaz Shamsi
01:31:21
Done3
Olivier Pourqiue
01:31:30
Done 3
Mahtab Dastpak
01:32:38
Done 3
Hassan Bukhari
01:32:47
Done 3
Rinaldo Catta-Preta
01:32:49
Done 3
accalia fu
01:37:26
done4
Laura Bricio Moreno
01:39:12
How do you hide the “all other cells’ cluster?
Rachel Battaglia
01:39:19
Done 4
Jacob Haase
01:39:29
done 4
Olivier Pourqiue
01:40:12
Done 4
Ayano Kohlgruber
01:40:25
done 4
Farnaz Shamsi
01:40:36
Done4
Sudhir Gopal
01:41:21
Done 4
Laura Bricio Moreno
01:41:33
Done 4
gabriela venturini da silva
01:41:34
don 4
Matthew Torre
01:41:35
Done 4
Annie Hsieh
01:42:05
Done 4
Rinaldo Catta-Preta
01:42:16
Done 4
Wonseok Lee
01:42:17
Done 4
Ayano Kohlgruber
01:42:23
is it possible in Cellenics to do T cell receptor analysis?
Hassan Bukhari
01:42:28
Done 4
Ayano Kohlgruber
01:42:34
or trajectory analysis similar to Monocle?
Vanitha Nithianandam
01:42:44
Done 4
Evanna Mills
01:43:08
dene 4
Ayano Kohlgruber
01:43:35
wonderful! thanks!
accalia fu
01:47:25
so I have the same genes but my heatmap intensities scale-wise look different (less yellow) and I cant figure out why..
Ayano Kohlgruber
01:47:38
ok great. my dataset focuses on CD4 and CD8 T cells from different tissues labeled via CITEseq with matched TCRseq. would be great to look at cell trajectory within a given CD4 or CD8 T cell population and overlay TCR clonotype information on a trajectory map (as one example of a type of analysis that would be really informative). will post my suggestion in the feedback section on the Cellenics portal! thank you!
Vicky Morrison - Biomage
01:48:50
Thanks Ayano!
Oliver Gibson - Biomage
01:50:51
Accalia, I’m not sure what might be the problem with the genes, but if you want to stick around for a couple of minutes after the workshop is over we can look into this
Oliver Gibson - Biomage
01:51:41
Actually, for the heatmap we select a random sample of the experiment, so it might be that different cells were selected than the ones shown in Alex’s experiment, leading to slightly different results
Oliver Gibson - Biomage
01:51:59
The trend should be similar, though. If that’s different then it’s definitely worth looking into!
Dana Vuzman
01:55:10
Thank you for participating in the Cellenics workshop! We will be in touch to collect your feedback on the workshop and the platform. In. The meantime, here are some helpful links:Cellenics Single Cell RNA-seq Analysis Platform link:https://scp.biomage.net/
Book a meeting to discuss your analysis:https://calendly.com/alexpickering/cellenics
Slides and exercises:https://drive.google.com/file/d/16WhdcNDvP3wdApII89qGKG5qArPAUdM2/view
gabriela venturini da silva
01:56:09
Thank you! The platform is amazing!
accalia fu
01:56:09
is this an alternative to tools in R or complementary..ie do you reccomend that I still learn the R tools?
Laura Bricio Moreno
01:56:31
Is there a link or a document explaining how to change the files from fast to the required ones?
Annie Hsieh
01:56:35
Thank you very much!
Olivier Pourqiue
01:56:42
Thank you !!!
Hassan Bukhari
01:56:54
Thank you!
Evanna Mills
01:56:59
thanks!
Farnaz Shamsi
01:57:09
This was great, thank you so much!
Ayano Kohlgruber
01:57:16
if we use Cellenics to analyze the RNAseq dataset, how should we cite the platform?
William Hou
01:57:35
Thank you, what should we cite if we use Cellenics?
Sudhir Gopal
01:57:42
This is pretty cool. Thank you all for this!
Majd Al Suqri
01:57:42
Thank you so much! This was very helpful
Alex Pickering
01:57:57
Thanks everyone! Get in touch :)
Rachel Battaglia
01:58:01
This is a fantastic tool. Thank you so much for the very helpful workshop!
Rinaldo Catta-Preta
01:58:23
thank you very much. congrats to the team. very nice job
accalia fu
01:58:36
Thanks very much, great tool and workshop!
Wonseok Lee
01:58:45
Fantastic job. Thank you for the workshop.
Dana Vuzman
01:59:34
We suggest including the following statement in your Methods section: "The single cell RNA-seq dataset was processed, explored and visualised using Cellenics® community instance (https://scp.biomage.net/) hosted by Biomage (https://biomage.net/)."We recommend that you report the processing settings (filtering thresholds, integration method, etc.) that are available for you to download via the 'Download' button in the Data Management module. We can assist with writing this paragraph, if needed. We can also provide the platform version number - just get in touch with us!And do keep us up-to-date with your submission and publication - we’d be delighted to hear about (and promote!) your paper!
Ayano Kohlgruber
02:00:14
Perfect! Really beautiful platform and super helpful module! Thank you everyone for your time!
William Hou
02:00:20
Thank you
Ying Liu
02:00:38
Thank you