User: xieshaojun0621

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Posts by xieshaojun0621

<prev • 29 results • page 1 of 3 • next >
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Add labels in the annotation bar of pheatmap
... I have the code below to generate the heatmap with annotation. ![enter image description here][1] library(pheatmap) # Generate some data test = matrix(rnorm(200), 20, 10) test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3 test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10 ...
labels annotation pheatmap heatmap written 7 days ago by xieshaojun062190 • updated 5 days ago by biostart240
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Differences of taxid and species_taxid in assembly_summary.txt
... In the file I downloaded here (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt ), there are two columns: taxid and species_taxid **What's the difference between these two columns?** Some of the lines these two columns are different: 391008 40324 Stenotrophomonas maltoph ...
genome assembly refseq ncbi written 23 days ago by xieshaojun062190
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Answer: A: KOBAS web server
... Once I also encountered the same problem. They fixed the problem after I sent an email to the author. At that time, they responded me very quickly. Currently Chinese New Year is there. Maybe they won't respond your email in the next couples days. ...
written 6 months ago by xieshaojun062190
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Answer: A: Integrating DMR data
... If you know how to use Linux, you can install BEDTools and use intersectBed to accomplish your task. ...
written 17 months ago by xieshaojun062190
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How to extract all the terms using summary?
... Hi there! I'm using clusterProfiler to do KEGG enrichment analysis. The function "enricher" was used. `res <- enricher(geneList, TERM2GENE=term2gene, TERM2NAME=term2name, pvalueCutoff = 1, pAdjustMethod = "BH", qvalueCutoff = 1)` Then the function "summary" was used to extract the results. `s ...
clusterprofiler written 17 months ago by xieshaojun062190 • updated 17 months ago by Guangchuang Yu1.9k
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Comment: C: How to define a non differentially expressed gene?
... Thanks for your response. But do you have any suggestions of how to achieve my goal? ...
written 17 months ago by xieshaojun062190
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Comment: C: Scaling data using Pheatmap
... Here is the functions in the [code][1] : scale_rows = function(x){ m = apply(x, 1, mean, na.rm = T) s = apply(x, 1, sd, na.rm = T) return((x - m) / s) } As you can see, scale in this package means removing the mean (centering) and dividing by the standard deviation ...
written 17 months ago by xieshaojun062190
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Comment: C: Scaling data using Pheatmap
... Why do you think pheatmap scales the data to mean 0 and standard deviation 3? ...
written 17 months ago by xieshaojun062190
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How to define a non differentially expressed gene?
... For example, I have C1, T1, C2 and T2 (each with triplicate). I ran DESeq2 to do pair-wise comparison. Now I'd like to extract the list of genes that show differentially expressed between C1 and T1, but non-differentially expressed between C2 and T2. For DEG, I can filter adj-pvalue and fold cha ...
deseq2 edger deg non-deg rna-seq written 17 months ago by xieshaojun062190 • updated 16 months ago by Michael Love1.6k
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Comment: C: Co-expression network for two time courses RNA-seq data
... Thanks for your quick response. I'll check WGCNA. ...
written 18 months ago by xieshaojun062190

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For How to install a specific version of R package in Bioconductor?
Popular Question 17 months ago, created a question with more than 1,000 views. For How to install a specific version of R package in Bioconductor?

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