User: krushnach80

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krushnach80690
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Posts by krushnach80

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Comment: C: How to draw boxplot with each point and background color by R ?
... your codes are lifesaver ...
written 4 weeks ago by krushnach80690
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Comment: C: How to draw boxplot with each point and background color by R ?
... https://www.biostars.org/p/284326/ ...
written 5 weeks ago by krushnach80690
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Comment: C: Intersect multiple bed and keep all fields
... A.bed chr1 817380 817560 + chr1 827560 827740 + chr1 867637 867817 + chr1 869928 870108 + chr1 904494 904674 + chr1 906813 906993 + chr1 912814 912994 + chr1 921200 921380 + chr1 923743 923923 + chr1 924685 924865 + B.bed chr1 826994 827076 + chr1 8 ...
written 7 weeks ago by krushnach80690
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Comment: C: ATAC-seq DE analysis
... I got it merging bam files you suggested if I use macs2. My doubt is if I have different bam files like from different condition when I merge them, how do I identify which bam file is from what condition ? ...
written 10 weeks ago by krushnach80690
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Comment: C: ATAC-seq DE analysis
... "Probably the safest is to merge all BAM files " never used it but how do I identify which bam file is what sample? ...
written 10 weeks ago by krushnach80690
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Comment: C: ATAC-seq sample normalization (quantil normalization)
... I asked my doubt on that thread .. ...
written 10 weeks ago by krushnach80690
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Comment: C: ATAC-seq DE analysis
... "peaks.narrowPeak" I got to this point but a little doubt, let say I have multi condition data ,so the "peaks.narrowPeak" would be combination of all the peak called by any peak calling tool .So to get the "peaks.narrowPeak" file do I have merge all the peak files or overlap the peak files ? ...
written 10 weeks ago by krushnach80690
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Comment: C: ATAC-seq sample normalization (quantil normalization)
... I tired to use rawcount once but later resorted to HOMER for all the analysis, I want to know how do you get raw counts from ATAC seq data ? I tried deeptools but it takes a bit of time not sure why...apart from deeptools I tired to use feature count but not able to do it.It is bit more complicated ...
written 10 weeks ago by krushnach80690
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Answer: C: differential network analysis
... WGCNA is the best place to start ...
written 3 months ago by krushnach80690
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Comment: C: WGCNA modules and categorical traits relationship
... i asked other WGCNA question , so here the caseControl is one of the data in the dataframe inside each module ..if i understand how the basic glm runs... ...
written 4 months ago by krushnach80690

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Popular Question 22 days ago, created a question with more than 1,000 views. For WGCNA code for chooseTopHubInEachModule
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Good Question 4 months ago, asked a question that was upvoted at least 5 times. For extract dendrogram cluster from pheatmap
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Popular Question 8 months ago, created a question with more than 1,000 views. For Java TreeView like tools
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: How to do the WGCNA in R
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Popular Question 10 months ago, created a question with more than 1,000 views. For WGCNA code for rna-seq data SFT plot issue
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