User: jarod_v6@libero.it

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Italy
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8 months ago
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Posts by jarod_v6@libero.it

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biomart not ound some prevous release
... Dear all, I need to annotate some rnaseq data from human. I use ensemble 74. On biomart I'm not able to found? It is normal? Why? listEnsemblArchives() name date url 1 Ensembl GRCh37 Feb 2014 http://grch37.ensembl.org 2 ...
rnaseq biomart written 8 months ago by jarod_v6@libero.it40 • updated 8 months ago by Mike Smith4.0k
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TCGA biomart conversion
... I want to convert ensembl ID to gene symbol using biomart. My ensemble ID are write with the version like this: ENSG00000066322.11 ENSG00000066336.10 ENSG00000066379.13   I have two problems: 1) Which the right version of ensembl to use for version of genome GRCh38.d1.vd1 2) How can extract ...
biomart written 16 months ago by jarod_v6@libero.it40 • updated 16 months ago by Mike Smith4.0k
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GenomicDatacommon execution error
... I Run this example: resp = cases() %>% filter(~ project.project_id=='TCGA-BRCA' & samples.sample_type=='Solid Tissue Normal') %>% GenomicDataCommons::select(c(default_fields(cases()),'samples.sample_type')) %>% response_all() count(resp)   I h ...
genomicdatacommon written 17 months ago by jarod_v6@libero.it40
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Biomart expection using values filter
... I use this code and seem I ca'nt filter only protein coding genes. If I use values= ret$ensembl the operation works well. How can resolve this problem ensembl = useMart( host="dec2017.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl" ) genemap <- getBM( ...
biomart written 17 months ago by jarod_v6@libero.it40 • updated 17 months ago by Mike Smith4.0k
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Maftotols importer error
... I try to import merged maf files . I have this error:   R version 3.4.1 (2017-06-30) -- "Single Candle" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute i ...
maftols written 18 months ago by jarod_v6@libero.it40
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problem on getpromoters on hg38
... I try to use ChIPseeker  I have peaks anntated with hg38.   library("ChIPseeker") library("TxDb.Hsapiens.UCSC.hg38.knownGene") setwd("~/Desktop/RESULTS2rip/") files=list.files("chr_hg38",full.names=T) files txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene peakfile=readPeakFile(files[1]) promoter < ...
chipseeker written 20 months ago by jarod_v6@libero.it40
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Comment: C: Deseq2 padj value very low
... thanks It was an error on the preparation on DESeqDataSetFromHTSeqCount so they not change that parameter. Thanks s much! ...
written 20 months ago by jarod_v6@libero.it40
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Comment: C: Deseq2 padj value very low
... thanks for the help.. the problem that I  have all the data are in that situation...         res<-results(dds) > head(res) log2 fold change (MLE): Intercept Wald test p-value: Intercept DataFrame with 6 rows and 6 columns baseMean log2FoldChange lfcSE stat p ...
written 20 months ago by jarod_v6@libero.it40
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Deseq2 padj value very low
... I have perform differential analysis using deseq2.  In the result I have many genes have very low padj. It is possible?   > res[which.min(res$padj),] log2 fold change (MAP): condition Myoepithelioma vs EMC Wald test p-value: condition Myoepithelioma vs EMC DataFrame with 1 row and 11 columns ...
deseq2 written 20 months ago by jarod_v6@libero.it40 • updated 20 months ago by Michael Love25k
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Comment: C: Sleuth error Error: Duplicate identifiers for rows
... Sorry, Please delete this question   ...
written 21 months ago by jarod_v6@libero.it40

Latest awards to jarod_v6@libero.it

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Popular Question 2.3 years ago, created a question with more than 1,000 views. For DESeq2 filter out my expression gene
Popular Question 2.3 years ago, created a question with more than 1,000 views. For txtimportData installation on R version 3.3.0 (2016-05-03)
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Pheatmap: how to use breaks for pheatmap
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Popular Question 3.7 years ago, created a question with more than 1,000 views. For Deseq2 PCA plot customize

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