User: rahel14350

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rahel1435030
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30
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New User
Location:
United States
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4 days, 4 hours ago
Joined:
4 years, 10 months ago
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r*********@gmail.com

Posts by rahel14350

<prev • 63 results • page 1 of 7 • next >
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Comment: C: Correlation between gene expression (RNAseq) and RRBS methylation data
... Well it is not quite the same (if I am correct) because in RRBS we have methylation value for each single site but in ATACseq we have the coverage for each peak region. I might can adapt it by using only the DMRs but then what will be the methylation value for each sample? the mean or median of all ...
written 25 days ago by rahel1435030
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Comment: C: Correlation between gene expression (RNAseq) and RRBS methylation data
... The main reason is that they (for example TCGAvisualize_starburst in TCGAbiolinks or COHCAP package) are for array data such as EPIC, 450K or 27K. ...
written 26 days ago by rahel1435030
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Correlation between gene expression (RNAseq) and RRBS methylation data
... Dear all, I have data from gene expression (RNAseq) and RRBS methylation data from mm10. I would like to calculate the Correlation between this data. There are many packages for TCGA data but they didn't work on my data. Do you know any other packages work on RRBS and RNAseq data? Kind Regards, Ra ...
R correlation rrbs rna-seq methylation written 26 days ago by rahel1435030 • updated 25 days ago by i.sudbery7.3k
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Answer: A: Enhancer identification in mm10 from RRBS data in R
... Deeptools based on region-scale helped me a lot. https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html ...
written 5 weeks ago by rahel1435030
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Comment: C: Enhancer identification in mm10 from RRBS data in R
... Many thanks for your reply. Then any tools like ngs.plot/compEPiTools are not useful in the case of RRBS data? ...
written 5 weeks ago by rahel1435030
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Enhancer identification in mm10 from RRBS data in R
... Dear all, Do you know any R packages that I can identify and visualize the enhancers from RRBS data in mm10? Kind Regards, Rahel ...
R enhancer visualization rrbs mm10 written 5 weeks ago by rahel1435030
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Comment: C: converting Bed to Wig
... Thank you so very much for your help. I will go try it but do you think in bedtools there is no problem with overlaps? ...
written 11 months ago by rahel1435030
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converting Bed to Wig
... Dear all, I want to convert a bed file to wig one for a better visualization on UCSC but I have an error (below). Do you have any idea how can I solve the error when I am aware of overlaps in the output file? library(rtracklayer) #bioconductor bed_loaded <- import.bed(con="diff.b ...
overlap bed wig bigwig rtracklayer written 11 months ago by rahel1435030 • updated 11 months ago by Alex Reynolds29k
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Comment: C: Applying machine learning algorithms on RNAseq data using MLSeq package or other
... What I want to do is classification and ranking of differentialy expressed genes (e.g. geneset-based approaches using SVM or RF). in MLSeq is mostly based on patient sample classification (train and test set) and I am not sure if I can use it for the gene set ....Can you please let me know which pac ...
written 12 months ago by rahel1435030
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Applying machine learning algorithms on RNAseq data using R
... Dear all, have you had any experience to apply machine learning algorithms on RNAseq output (Gene set approached not sample base approaches)? What is the packages or program you used for it? I found this MLSeq package that help to apply machine learning approaches on RNAseq data based on patient s ...
rnaseq mlseq svm machine learning rf written 12 months ago by rahel1435030

Latest awards to rahel14350

Popular Question 4 months ago, created a question with more than 1,000 views. For categorize DMRs by type (hyper - hypo methilated) in DMRcate or minfi
Popular Question 4 months ago, created a question with more than 1,000 views. For visualization of DMRcate or minfi output on UCSC
Popular Question 4 months ago, created a question with more than 1,000 views. For converting to MAF or clustal format
Popular Question 6 months ago, created a question with more than 1,000 views. For converting to MAF or clustal format
Popular Question 7 months ago, created a question with more than 1,000 views. For converting to MAF or clustal format
Popular Question 11 months ago, created a question with more than 1,000 views. For Plotting numbers of somatic substitutions per megabase (MB)
Popular Question 13 months ago, created a question with more than 1,000 views. For converting to MAF or clustal format
Popular Question 18 months ago, created a question with more than 1,000 views. For converting to MAF or clustal format
Popular Question 19 months ago, created a question with more than 1,000 views. For Plotting numbers of somatic substitutions per megabase (MB)
Popular Question 20 months ago, created a question with more than 1,000 views. For Plotting numbers of somatic substitutions per megabase (MB)
Scholar 2.7 years ago, created an answer that has been accepted. For A: RRBS data analysis using RnBeads give Scan() error

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