User: krushnach80

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krushnach80160
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Posts by krushnach80

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Comment: C: ggscatter two color issue
... can you tell me how do i just label the samples p + gradient_color(c("red", "blue")) i m using this...but it seems its labelling the genes not the samples... ...
written 7 days ago by krushnach80160
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ggscatter two color issue
... data1 <- AVERAGE_HSC_LSC data1$HSC <- as.factor(data1$HSC) library("ggpubr") ggscatter(data1, x = "HSC", y = "LSC", color = "HSC", shape = "HSC", add = "reg.line", conf.int = FALSE, palette = c("#00AFBB"), cor.coef = TR ...
R written 7 days ago by krushnach80160
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Comment: C: ATAC seq specific region extraction
... I have done that I mean see those region in IGV > If you want instead to plot specific regions with deepTools then use only those as input into computeMatrix cani I do that for specific regions ? I mean lets say I want to see what is happening with chr 7 and can I plot the same with the compute ...
written 7 days ago by krushnach80160 • updated 7 days ago by Devon Ryan70k
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ATAC seq specific region extraction
... I have set of induced vs induced atac seq data , i did try to plot the tss region with deeptools i was able to do but i want to extract specific promoter regions .How can i do that what tools do i use to do the same ?I want to see at particlular promoter site how the chromosome region is ,is it open ...
chip-seq written 7 days ago by krushnach80160 • updated 7 days ago by Devon Ryan70k
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Comment: C: expression to networking
... well yes....but apart from that ?anything i have this flowchart can you give me more insight [flowchart][1] [1]: https://www.hindawi.com/journals/bmri/2016/8313272/fig1/ ...
written 9 days ago by krushnach80160
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expression to networking
... I would like to know how to proceed from my gene expression data to building a network from that expression data . So far what im doing is checking the differential expression of genes and see how it changes ..but that wont give me a global picture i suppose ..So it would be helpful if anyone can ...
rna-seq written 10 days ago by krushnach80160 • updated 9 days ago by mforde84810
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Comment: C: Fold change UP and Down in dplyr calculation
... thankyou for making it clear ...
written 13 days ago by krushnach80160
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Comment: C: Fold change UP and Down in dplyr calculation
... c(-Inf, -2.5, 2.5, Inf), include.lowest = TRUE, labels = c("DOWN", "NC", "UP")) can you explain ..this so if i get -2.5 then down and 2.5 .....but when do i get NC? ...
written 13 days ago by krushnach80160
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Comment: C: Fold change UP and Down in dplyr calculation
... thank you for the code since i have pretty basic use of R i dont know how these simple yet effective things to do...but thank you again ...
written 13 days ago by krushnach80160
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Comment: C: Fold change UP and Down in dplyr calculation
... where do i include your code in my code cut(logFC, breaks = c(-Inf, -2.5, 2.5, Inf), include.lowest = TRUE, labels = c("DOWN", "NC", "UP")) can you tell me ...? ...
written 13 days ago by krushnach80160

Latest awards to krushnach80

Voter 6 months ago, voted more than 100 times.
Centurion 6 months ago, created 100 posts.
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: differential gene expression analysis
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