User: rahel14350

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rahel1435030
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New User
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United States
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1 day, 4 hours ago
Joined:
3 years, 10 months ago
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Posts by rahel14350

<prev • 55 results • page 1 of 6 • next >
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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 1 day 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 1 day ago by rahel1435030
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Comment: C: R packages for Data mining or machine learning of a set of differentialy express
... Many thanks, this paper could be helpful! I am going to check it. ...
written 8 weeks ago by rahel1435030
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Comment: C: R packages for Data mining or machine learning of a set of differentialy express
... Dear Arup, Pathway analysis is not a part of Data mining/machine learning. I am looking for some packages to apply SNV or RF or Neural network algorithms on RNAseq data. Many thanks ...
written 8 weeks ago by rahel1435030
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R packages for applying Data mining or machine learning algorithms (SNV,RF, Neural Network) on RNAseq data
... Dear all, I have a set of differentially expressed genes. I want to use Data mining/machine learning R packages to see which set or pairs of genes are more related to each other on the function (to classify them and find potential biomarkers)? Basically to apply SNV, random forest and neural network ...
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Comment: C: count tables from RNA-seq data on GEOmetadb
... Dear Sean, Many thanks for your prompt reply. I did also tried GEOquery but I need to do it per study (GSE*) and then I can use Limma. I can not get the table counts for all of the studies using getGEO(). I also can combine/merge two eset but when they are on the same platform or the number of sampl ...
written 7 months ago by rahel1435030
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count tables from RNA-seq data on GEOmetadb
... Dear https://www.biostars.org/u/287/, I would like to work on the count tables of normal and metastatic samples of Colon (Colorectal) cancer using RNA-seq. I tried this code from GEOmetadb but I did not get all the information. Do you think is there anyway I can address all the data that I want like ...
geometadb geo geoquery sradb rna-seq written 7 months ago by rahel1435030 • updated 7 months ago by Sean Davis25k
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Comment: C: Differentially methylated regions (DMRs) and sites (DMCs) are not in the same re
... Many thanks for your reply. Now it is more clear for me why I have such an output. ...
written 9 months ago by rahel1435030
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Comment: C: Differentially methylated regions (DMRs) and sites (DMCs) are not in the same re
... Thanks a lot for your reply. I was running all different packages and having the same result, now it is clear for me. ...
written 9 months ago by rahel1435030
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Differentially methylated regions (DMRs) and sites (DMCs) are not in the same region
... Dear all, I have some RRBS data with very low coverage and high number of NAs which they are aligned with BSMAP (more than 900,000 rows contain NAs). I did try many different packages but in all of them the DMRs and DMcs are completely different for example if gene A is detected as significantly me ...
metilene rrbs rnbeads methylkit written 9 months ago by rahel1435030 • updated 9 months ago by Devon Ryan88k

Latest awards to rahel14350

Popular Question 5 weeks ago, created a question with more than 1,000 views. For converting to MAF or clustal format
Popular Question 5 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 Plotting numbers of somatic substitutions per megabase (MB)
Popular Question 8 months ago, created a question with more than 1,000 views. For Plotting numbers of somatic substitutions per megabase (MB)
Scholar 19 months ago, created an answer that has been accepted. For A: RRBS data analysis using RnBeads give Scan() error

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