User: rahel14350

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rahel1435020
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New User
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United States
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1 day, 2 hours ago
Joined:
2 years, 8 months ago
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Posts by rahel14350

<prev • 39 results • page 1 of 4 • next >
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Comment: C: annotation of RRBS DMRs in RnBeads or other packages
... I used package annotatr and it helped me. https://bioconductor.org/packages/release/bioc/vignettes/annotatr/inst/doc/annotatr-vignette.html ...
written 2 days ago by rahel1435020
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annotation of RRBS DMRs in RnBeads or other packages
... I used the mean methylation value and Wilcox test to define differentially methylated regions between two groups of RRBS data. Is there any way that I could import the Granges from DMRs to RnBeads to annotate them there? Or do you have any suggestion for which package I could use only for annotation ...
annotation dmrs rrbs rnbeads granges written 6 days ago by rahel1435020
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filtering (deleting) the overlapped genomic ranges from two GRangelist using findOverlaps
... Dear all, I have two Grnage list (gr2=repeatmask.hg38 from UCSC; gr1=CpGs methylation regions from RRBS data). I want to filter out the CpGs that are in the genome repeated regions. I did it like this, do you think if it is correct? > hits <- findOverlaps(gr2, gr1) > head(hits) Hits obj ...
genomicranges findoverlap overlapped written 10 weeks ago by rahel1435020
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KNIME workflow for data mining of protein expression data from TCGA
... Dear all and Dear https://www.biostars.org/u/30/ Do you know if there Is any workflow available in KNIME for data mining using protein expression data from TCGA to identify biomarkers? Many thanks in advance, Rahel ...
knime data mining protein biomarker tcga written 5 months ago by rahel1435020
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Answer: A: categorize DMRs by type (hyper - hypo methilated) in DMRcate or minfi
... Dear all, I got this answer on the google groups from Dr. Tim Triche and it worked for me. I add it here, in case any one of you had the same question. ... yes, of course. And I say this having used both the DSS-backed N=1 DMR calling approach and also DMRcate's approach on the same pediatric samp ...
written 5 months ago by rahel1435020
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Comment: C: deconvolution of heterogenous cell types in RRBS data
... Dear Davon, I am not sure If you see my answer via e-Mail. I deleted it because I did not get any answer and I have many of those questions without answer! I can write it again if it was useful. By the way there is MeDeCom package out and I am trying that on RnBeads data and I hope to use it for Co ...
written 5 months ago by rahel1435020
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missing values for beta values in Rnbeads (imputation of NAs)
... Dear all, I have many NAs in the Methylation matrix from RnBeads. Is there anyway to remove this NAs or impute them? Many Thanks, Rahel ...
na beta values rnbeads methylation values written 5 months ago by rahel1435020
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Answer: A: RRBS data analysis using RnBeads give Scan() error
... So, I found the solution, The reason was that I forgot to define "import.bed.style" like this: rnb.options(import.bed.style= "EPP") Now everything is working as usual without error! ...
written 5 months ago by rahel1435020
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RRBS data analysis using RnBeads give Scan() error
... Dear all, I am working on RRBS data using RnBeads but in the beginning of the analysis I have this Error from R: > result <- rnb.run.analysis(dir.reports=report.dir, data.source=data.source, data.type="bs.bed.dir") 2017-07-31 15:12:51 1.0 STATUS ...
450k scan() rrbs rnbeads written 5 months ago by rahel1435020
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Comment: C: biomarkers identification by data mining of public genomic tumour databases in R
... Dear Kevin, Many thanks for your reply. I am going to check them ... ...
written 7 months ago by rahel1435020

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Scholar 5 months ago, created an answer that has been accepted. For A: RRBS data analysis using RnBeads give Scan() error

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