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Glad you like it

Thank you ☺️

Thanks for liking

Please email to company directly

It needs paid subscription

@asifmolbio but i got academic license

@ it should be okay then, did you use log in and password?

@asifmolbio yes

yes equally applicable to proteomics data as well

While using zilla, are you sure you accessed the folder rightly ?

@@asifmolbio Sir, thank you so much for helping at zoom meeting

Did you enter them in fist column?

@asifmolbio once I put in row it was not coming.. Even though I use the SRPLOT demo excel; protein or gene names are not coming

I am not sure if any

Then use tissue sample as different treatments

@@asifmolbio and anyone tissue keep as control for double delta calculation?

Glad you enjoyed it

No need to cancel. A few days ago, i did for 42 sequences it took almost 7 hours

If you have Mac book it would be quick

This metadata needs to create by yourself in excel, i have explained in this same video to how to prepare

Yes it can download all the sizes as long as your directory have space

This feature is not available, only copy paste option is working

Yes if the option is not available in the journal's website/dashboard you can directly email to editor

Email to administrator he will recharge it for free

@@asifmolbio thanks

Thanks for your kind words!

Hello Manuel, Thank you for your question, and I’m happy to help you clarify things further! Mantel’s r (the Mantel correlation coefficient) is quite similar to Pearson’s r in that it measures the strength and direction of the linear relationship between two distance matrices. Essentially, it quantifies how similar the distances between pairs of objects are across two different datasets or variables. If r is close to +1 or -1, it indicates a strong relationship, while a value near 0 indicates no significant relationship. Now, regarding Mantel's t, it's a test statistic used in the Mantel test, which is essentially a permutation test to assess the significance of the observed Mantel correlation. While r tells you about the strength of the relationship, t is the value that you compare against a distribution of values generated by randomly permuting the data. The larger the t value, the more likely your observed r is not due to random chance. To summarize: Mantel’s r: Correlation coefficient, like Pearson's r, showing how related two distance matrices are. Mantel’s t: The test statistic that is used in permutation testing to determine the statistical significance of r. If you have further questions or need additional clarification, feel free to ask! Best regards, Dr. Asif

Mantel's test is used to assess the correlation between two distance matrices, allowing researchers to determine whether there is a significant relationship between the distances (or dissimilarities) between objects in two different datasets. It is commonly used when you have data in the form of distance or dissimilarity matrices, which could represent, for example, genetic distances, ecological distances, or spatial distances between samples. Here are some key reasons why Mantel's test is used: Comparing Dissimilarities: Mantel's test allows you to compare the pairwise dissimilarities or distances between objects across two different datasets. For example, in ecology, you might want to test if geographic distances between sampling sites correlate with differences in species composition. Testing Non-Linear Relationships: While Pearson's correlation is used for linear relationships, Mantel’s test can be used for non-linear relationships as long as the data are represented in distance matrices. Handling Complex Data: Mantel’s test is particularly useful when working with complex datasets where you don’t have a direct correspondence between variables. For example, it’s widely used in fields like genomics, ecology, and evolutionary biology to explore relationships between genetic, environmental, and geographical data. Permutation-Based: The test is based on permutations, which allows you to assess the statistical significance of the observed correlation without making assumptions about the underlying distributions of the data. In summary, Mantel's test is valuable when you want to assess the correlation between two distance matrices, especially when the data is complex or non-linear, and it’s used widely in ecological, genomic, and evolutionary studies.

Sure thank you so much for suggesting a good topic

Usually there are restriction of number of pages but no restirction of fonts. So i would recommend time new roman 12, with spacing 1.5 or 2.

@@asifmolbio Thank you Dr Asif, what is the exact page restriction for number of pages, and how should it be strcutured? is there a template you could share, as my login details do not work? Thank you

Share your email i will send you a draft

:p

Sure InshaAllah

Glad you like it

Glad you like it

Thanks and welcome

Please check previous video on genome wide analysis for phylogenetic analysis by MEGA, its explained

Watch full video i have already explained

Sure i will record

for practice purpose you can select anyone, but if you want to go for a research article then off course you need to select first any family which is not published already

@@asifmolbio that's mean if i select s. melongena for my publications, i have to take solanacae family crops for phylogenetic tree?

Glad if its helping

Glad if it’s helpful

Thanks

Thanks

Yes exactly

Still can apply, proposal is more important.

thanks a lot brother ❤❤

proteins IDs and FC value

Protein IDs and abundace in samples (including replicates)

Sir can I contact you because I have some issue regarding this how can I contact you I am involved in various research work related to pharmacology

Just write it in the brackets and submit it back. they will publish with your ORICID

No you are the first one

How many species and proteins are there in your tree?

@@asifmolbio My circular tree has 50 TEF 1 alpha sequences. I added my tree in nwk format to Chiplot. I added my excel sheet (metadata) to Chiplot: Column 1 (sequences); column 2 (categories A, B, C). My idea is to group the sequences with colors with their respective category (color block of leaves name) min 10.30 in the video. In the figure I only get the legend with three colors, but the graph is not drawn. Greetings and thank you very much for answering me!

Can change selection threshold to FC >1 and re analyze data on iDEP tool

Thanks for generous message. By the way i am from Pakistan 🇵🇰

Yes i am planning these videos, stay tuned

It depends, in most of cases will not

@@asifmolbio thank you Sir

There are alot of videos which already covered theory part

Both (with and without) options can be used

Check this out

How to a scale bar to microscopic images by Image J software th-cam.com/video/kVqVSkh_hwE/w-d-xo.html

Thanks, you are right. I was busy. let me know if you have any questions