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Creating a Heatmap in R | ComplexHeatMap tutorial p1

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LiquidBrain Bioinformatics

LiquidBrain Bioinformatics

Күн бұрын

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@PeihuiBrandonYeo
@PeihuiBrandonYeo 3 жыл бұрын
0:00 Introduction to video content 1:08 Why the R markdown format 1:33 installing package and loading ComplexHeatmap into R 2:40 Making the data matrix 3:23 Heatmap() on all default settings 4:40 Changing the colors 6:50 Dealing with outliers in heatmap- data transformation 7:48 RAINBOW!! 8:40 Discrete matrix 10:26 Dealing with NA in data 11:20 Columns and row tittles 12:22 Clustering dendrogram 13:10 Size of dendrogram 14:40 clustering function 15:37 Using dendextend 17:25 Reordering rows , row and column tittles 20:57 row or columns split 24:30 Putting everything together
@user-cg4gk9np2p
@user-cg4gk9np2p 2 жыл бұрын
Hi at 22.09 min for the kmean clustering does the dendrogram based on Hierarchical clustering or kmean ?
@AlexPreboy
@AlexPreboy 2 жыл бұрын
Please consider saying no to background music
@williamvilchezcruz
@williamvilchezcruz 11 ай бұрын
Excellent tutorial 😊
@M1m1i1
@M1m1i1 3 жыл бұрын
Nice tutorial! Waiting for pt2
@brucekang6474
@brucekang6474 2 жыл бұрын
awsome tutorial!! waiting for pt2
@LiquidBrain
@LiquidBrain 2 жыл бұрын
Oh, you can find all 4videos on the channel already
@neurostudywithme
@neurostudywithme Жыл бұрын
thank you. but how can I sort my heat map based on my marker genes per cluster. In articles they show a very nice heat map figure where the expression of genes per cluster goes like a line..how can I do that
@paolamontenegro517
@paolamontenegro517 Жыл бұрын
Hi, I have the same question, Do you maybe get any answer?
@neurostudywithme
@neurostudywithme 10 ай бұрын
@@paolamontenegro517 Hi! Yea so what I'm doing is first I Find marker genes and make list for each cluster and using this list as features when I'm generating heat map. Also you can sort your clusters based on similarty
@mebratuify
@mebratuify Жыл бұрын
How can we do heatmap spearman correlation graphs? Thank you so much.
@darshiv_
@darshiv_ Жыл бұрын
hello, how can we sort the x axis values in alphabetical order ? my files are named form r1 to r9 and they are not in order.
@hanifullah1088
@hanifullah1088 2 жыл бұрын
Actually i have gene expression data of about 19000 gene and 90 samples, so i want to know how can i narrow down my expression data ?
@LiquidBrain
@LiquidBrain 2 жыл бұрын
There are many ways to do that as it depends on the purpose of your research. The easiest way is to remove the low expression genes, or run a PCA or other dimensional reduction analysis and check the loading of the genes, which then, you can remove the genes with the least loading since it doesn't contribute to the separation of the different sample.
@killa14108
@killa14108 2 жыл бұрын
@@LiquidBrain Can you do a tutorial on doing a PCA on a big gene expression data set? I really want to know how to do the PCA analysis and how to actually reduce the dimension of my data set with PCA with code examples! Would be doing me a big favor!
@LiquidBrain
@LiquidBrain 2 жыл бұрын
@@killa14108 I just uploaded a video on limma voom pipeline, that should be able to help you on this analysis
@johnathonmcl
@johnathonmcl 2 жыл бұрын
Can the matrix be loaded in from an excel file? Will this hinder the rest of the code? Thanks for the great videos
@LiquidBrain
@LiquidBrain 2 жыл бұрын
As long as the data structure looks the same after you input, it should not actually matter :)
@johnathonmcl
@johnathonmcl 2 жыл бұрын
@@LiquidBrain thank you for your reply! I am going to test the code out today, just one more question, could you possibly show how to clacupate the confidence interval to plot alongside the heatmap? Or are there any good resources that might help me with that?
@johnathonmcl
@johnathonmcl 2 жыл бұрын
Calculate*
@lvn2410
@lvn2410 Жыл бұрын
Help all my damn colnames have pasted together and copied onto every column aidhdvdv they’re not individual!!!!
@smraza9
@smraza9 3 жыл бұрын
Hi can you make a video on diagonally split tiles heatmaps in seaborn and triangulation packages of python
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