User: mbk0asis

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mbk0asis610
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Posts by mbk0asis

<prev • 164 results • page 1 of 17 • next >
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Answer: A: circos error - no change to housekeeping.conf
... I'm not sure if this can help you, but I found following sentence in the [circos best practice page][1]. "If your data is sampled more finely than this, you will not see any structure in it because multiple data points will be assigned to the same pixel. In general, if you have more than 10,000 dat ...
written 9 weeks ago by mbk0asis610
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Comment: C: how to create mutant DNA sequence
... Hi! Thank you for reply! I used `substring` in R to replace a string at a specific position. substring(test$WT.seq, first=5) <- "G" It replaces a string in the 5th position to "G". It's not the actual code I used, but the approach is the same. ...
written 11 weeks ago by mbk0asis610
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how to create mutant DNA sequence
... Hi, all! I'm trying to generate mutant sequence based on the type as shown on the far right column of example data below. transcript position mutation type WT.seq MUT.seq trx1 5 A>G substitution AAAAAA AAAAGA trx2 3 C>CTT insert CCCCCC CCCTTCCC trx3 7 TTTT>T deletion AAAAA ...
in silico mutagenesis mutation written 11 weeks ago by mbk0asis610
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Comment: C: Adding gene set to GSVA
... Great post here! I was looking for exactly the same answer! To get gene sets in ENSEMBL ids, what can I do? Thank you! ...
written 6 months ago by mbk0asis610
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Comment: C: GSVA example leukemia returns a 'NULL' object
... Thank you, Kevin! That was exactly the problem here! Apparently, I was following an old tutorial. ...
written 6 months ago by mbk0asis610
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GSVA example leukemia returns a 'NULL' object
... Hello! While I tested GSVA using the example dataset, I encountered a problem. Function 'gsva' returned 'NULL', no further analysis could be processed. I just copied the codes form the vignette and ran it as described. I pasted the codes under this question. Could someone help me? Thank you! ...
gsva rna-seq written 6 months ago by mbk0asis610 • updated 6 months ago by Kevin Blighe71k
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WGCNA - consensus analysis - cutreeStatic - no samples selected
... Hello! I'm currently trying to identify consensus gene sets between two different tissue types, Muscle/PBMC, using WGCNA. I have two normalized count matrices from DESeq2 for each tissue type. I simply transposed them and made a list as written in the tutorial. > nSets = 2; > ...
wgcna rna-seq written 7 months ago by mbk0asis610 • updated 24 days ago by jfaberha0
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Comment: C: Odd DESeq2 results
... After carefully checking the data, I found that I got different normalized count values depending on the samples. I have 36 samples in 5 groups as follow (for simplicity, I changed the sample names to more easily distinguish them), HD_old_1 HD_old_2 HD_old_3 HD_old_4 HD_old_5 ...
written 7 months ago by mbk0asis610
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Comment: C: Seurat3 DimPlot inconsistency
... Thank you, António! I will do that~~ ...
written 8 months ago by mbk0asis610
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Seurat3 DimPlot inconsistency
... Hi, all! I'm currently analysing a single cell RNA-seq data using Seurat3. While analysing, I found that the UMAP/tSNE plots by `DimPlot` kept changing everytime I ran it even though I sat the `seed.use` for `RunPCA` and `RunUMAP`. The code I used is below. >nDim = 50 >mipsc <- ...
seurat3 rna-seq seurat written 8 months ago by mbk0asis610

Latest awards to mbk0asis

Popular Question 15 days ago, created a question with more than 1,000 views. For How to mark mutation sites?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How to mark mutation sites?
Great Question 6 weeks ago, created a question with more than 5,000 views. For How to remove a chr from a bam file?
Epic Question 7 weeks ago, created a question with more than 10,000 views. For Finding a sequence in a fasta file
Popular Question 9 weeks ago, created a question with more than 1,000 views. For How to split numbers and strings?
Popular Question 4 months ago, created a question with more than 1,000 views. For How to mark mutation sites?
Popular Question 4 months ago, created a question with more than 1,000 views. For Batch replcement of fasta header
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Subsetting DESeq2 results by padj quantity
Popular Question 4 months ago, created a question with more than 1,000 views. For How to split numbers and strings?
Popular Question 10 months ago, created a question with more than 1,000 views. For bash for loop with two type of files
Popular Question 11 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Popular Question 13 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Voter 13 months ago, voted more than 100 times.
Great Question 13 months ago, created a question with more than 5,000 views. For How to remove a chr from a bam file?
Popular Question 15 months ago, created a question with more than 1,000 views. For Where can I get bovine 'kegg.gs' in R?
Popular Question 16 months ago, created a question with more than 1,000 views. For new line to tab in every second column
Popular Question 16 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Popular Question 19 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Student 19 months ago, asked a question with at least 3 up-votes. For fasta - reverse complement sequence
Popular Question 19 months ago, created a question with more than 1,000 views. For bash for loop with two type of files
Popular Question 21 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Popular Question 22 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Popular Question 23 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Epic Question 2.0 years ago, created a question with more than 10,000 views. For Finding a sequence in a fasta file
Great Question 2.2 years ago, created a question with more than 5,000 views. For fasta - reverse complement sequence

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