User: rahel14350

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rahel1435030
Reputation:
30
Status:
New User
Location:
United States
Last seen:
2 weeks, 2 days ago
Joined:
5 years, 6 months ago
Email:
r*********@gmail.com

Posts by rahel14350

<prev • 65 results • page 1 of 7 • next >
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Comment: C: ATACseq libraries differ in each run
... Thanks a lot for your reply. ...
written 5 months ago by rahel1435030
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ATACseq libraries differ in each run
... Dear all, I did some ATACseq last year and we wanted to repeat it this year using the same isolation and preparation kits but the libraries looks so different. Is there anybody had the same experience and if you advice to do the sequencing based on this libraries? Many thanks in advance, Rahel ![ent ...
atacseq chip-seq library sequencing written 5 months ago by rahel1435030
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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 8 months 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 9 months 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 9 months ago by rahel1435030 • updated 9 months ago by i.sudbery9.8k
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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 9 months 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 9 months 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 9 months 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 19 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 19 months ago by rahel1435030 • updated 19 months ago by Alex Reynolds31k

Latest awards to rahel14350

Popular Question 8 months ago, created a question with more than 1,000 views. For Correcting batch effect from known variables in RnBeads using Combat
Popular Question 8 months ago, created a question with more than 1,000 views. For visualization of DMRcate or minfi output on UCSC
Popular Question 8 months ago, created a question with more than 1,000 views. For converting to MAF or clustal format
Popular Question 8 months ago, created a question with more than 1,000 views. For deconvolution of heterogenous cell types in RRBS data
Popular Question 12 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 12 months ago, created a question with more than 1,000 views. For visualization of DMRcate or minfi output on UCSC
Popular Question 12 months ago, created a question with more than 1,000 views. For converting to MAF or clustal format
Popular Question 14 months ago, created a question with more than 1,000 views. For converting to MAF or clustal format
Popular Question 15 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 22 months ago, created a question with more than 1,000 views. For converting to MAF or clustal format
Popular Question 2.2 years ago, created a question with more than 1,000 views. For converting to MAF or clustal format
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Plotting numbers of somatic substitutions per megabase (MB)
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Plotting numbers of somatic substitutions per megabase (MB)
Scholar 3.3 years ago, created an answer that has been accepted. For A: RRBS data analysis using RnBeads give Scan() error

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