User: antgomo

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antgomo30
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Spain
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6 months ago
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Posts by antgomo

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Is Kallisto able to deal with UMIs and paired-end RNASeq?
... Exactly, that's what I read. And is the the same that I put on batch.txt as you can see in my post, the point then (what i was asking) is if Kallisto is only able to deal with UMIs in single end mode (i.e first file UMI and second one FASTQ). ...
written 6 months ago by antgomo30
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Is Kallisto able to deal with UMIs and paired-end RNASeq?
... Hi All, i have a paired-end bulk RNAseq generated with UMIs in order to reduce duplicates from PCR Since now, i used my own piepeline with STAR + UMI_tools to deal with the UMIs and generate a "clean duplicates " bam file, but I wnat to know if kallisto is able to deal with this data I have three ...
umi kallisto rna-seq written 6 months ago by antgomo30 • updated 6 months ago by genomax68k
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Answer: A: ROC curve for biomarkers
... So, your idea will be (correct me if I am wrong): Imagine you have a set of 2000 DE genes from your DEseq2 analysis and you want o go iteratively generating subsets of 7-10 genes that enter in randomForest/SVM feature classification of samples, and the group/combinaion of genes which reach a AUC of ...
written 17 months ago by antgomo30
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Clustering genes in time course analysis according slopes in quadratic regression model
... I have a RNA time course experiment, 7 time points, 2 replicates per point. After analyzed with DESeq2 package, I want to subset my results in 4 categories 1. Those genes that are increasing expression lineally from time 0 to 7 2. Those genes that are decreasing expression lineally from time 0 to ...
quadratic regression time course gene expression written 3.4 years ago by antgomo30 • updated 3.3 years ago by Biostar ♦♦ 20
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Comment: C: Heatmap of Agilent two colors Dye Swap experiment
... OK. Thanks Manu, but this is not the point. I got my diff expressed genes, and I know to build the heatmap. The problem is that I have my R and S samples distributed in different channels and what I want to see is my heatmap of R and S, maybe I was no clear at this point, not see how A,B and C (arra ...
written 4.6 years ago by antgomo30
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Heatmap of Agilent two colors Dye Swap experiment
... Hi, I have an Agilent Dye Swap experiment, two colors, where I have my samples Resistant and Sensible Distributed like this (this is my targets.txt file) SampleNumber FileName Cy3 Cy5 1 A.txt S R 2 B.txt R S 3 C.txt S R 4 D.txt R S 5 E.txt S R ...
array agilent two colors heatmap written 4.6 years ago by antgomo30 • updated 4.3 years ago by Biostar ♦♦ 20
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Comment: C: Chippeakanno Distance To Tss In Up And Downstream
... Sorry again for the questions, but probably is a point important that I missed in all the conversation. When I was talking about downstream and upstream is not about the strand orientation but the TSS that are upstream and downstream for this particular DMR in positive strand and the same for the ne ...
written 5.2 years ago by antgomo30
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Comment: C: Chippeakanno Distance To Tss In Up And Downstream
... done it, tss.upstream <- tss.gr[tss.gr@strand == "+"] tss.downstream <- tss.gr[tss.gr@strand == "-"] ...
written 5.2 years ago by antgomo30
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Comment: C: Chippeakanno Distance To Tss In Up And Downstream
... Thanks! but I got problems subsetting TSS by strand, strand is not a metadata column ...
written 5.2 years ago by antgomo30
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Comment: C: Chippeakanno Distance To Tss In Up And Downstream
... I tried and I didn't get more than one TSS, and I a expecting both, one upstream DMR and one downstream. Maybe is a silly question what I am asking to, but it is possible? ...
written 5.2 years ago by antgomo30

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Popular Question 14 months ago, created a question with more than 1,000 views. For Chippeakanno Distance To Tss In Up And Downstream
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Chippeakanno Distance To Tss In Up And Downstream
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Heatmap of Agilent two colors Dye Swap experiment
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Popular Question 4.6 years ago, created a question with more than 1,000 views. For Get Non-Synonymous Point Mutations From Cosmicmart
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Chippeakanno Distance To Tss In Up And Downstream

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