User: skjobs0123
skjobs0123 • 170
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Posts by skjobs0123
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... Hi Kevin
How calculate FDA in COX-PH regression!!!?
...
written 7 weeks ago by
skjobs0123 • 170
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... How do calculate FRD value from p-value using COX-PH. Is there any direct function in R to calculate FDR value. using this script given below
BRCA <- read.table("BRCA.txt", header = TRUE, sep=',')
fit_model <- survfit(Surv(OS_MONTHS, OS_STATUS) ~ SEX, data = file)
summary(fit_mod ...
written 7 weeks ago by
skjobs0123 • 170
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... Hi,
I have a heatmap which is generated by complexheatmap R library. We have 3 clusters (cluster1, cluster2 and cluster3) in a heatmap in figure. I want to further amplify the cluster3 only. ![heatmap][1]
[1]: https://i.ibb.co/pLpb0fM/Rplot056.png ...
written 9 months ago by
skjobs0123 • 170
• updated
9 months ago by
GenoMax ♦ 94k
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Comment:
C: Downstream RNA seq analysis
... You can do a lots of things in down stream process such as gene ontology, pathways analysis, protein protein interaction or you can see how many of the genes are belong to which classes of protein and family. The question is very generic please make precise. What really you want. ...
written 11 months ago by
skjobs0123 • 170
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... Use biodbnet to convert biological ID and then you can fetch from entrez or other site.
https://biodbnet-abcc.ncifcrf.gov/db/db2db.php
...
written 12 months ago by
skjobs0123 • 170
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... Use this code to generate heatmap
# Use RColorBrewer color palette names
library("RColorBrewer")
col <- colorRampPalette(brewer.pal(10, "RdYlBu"))(256)
heatmap(df, scale = "none", col = col,
RowSideColors = rep(c("blue", "pink"), each = 16),
...
written 12 months ago by
skjobs0123 • 170
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... Use HIPPIE database ([http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/][1]) for PPI interaction, Or string. First, mapped Gene ID with these database and then upload table into Cytoscape. Further, you can do whatever you want.
[1]: http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/ ...
written 12 months ago by
skjobs0123 • 170
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Comment:
C: query on salmon installation
... then set the PATH in ~/.bashrc
...
written 12 months ago by
skjobs0123 • 170
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... You can use this tutorial
[http://cole-trapnell-lab.github.io/monocle-release/monocle3/][1]
...
written 12 months ago by
skjobs0123 • 170
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... Thanks, Samples are not homogeneous like:
Sample Condition Machine
1 Control Hiseq
2 Control Hiseq
3 Control Nextseq
4 Control Nextseq
5 Treatment Hiseq
6 Treatment Hiseq
7 Treat ...
written 12 months ago by
skjobs0123 • 170
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For WGCNA Network Analysis
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For A: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
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For A: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
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