User: VHahaut

gravatar for VHahaut
VHahaut990
Reputation:
990
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Trusted
Location:
Belgium
Twitter:
Vincent_Hahaut
Last seen:
an hour ago
Joined:
2 years, 3 months ago
Email:
v*************@gmail.com

Posts by VHahaut

<prev • 114 results • page 1 of 12 • next >
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Comment: C: How to extend the heatmap data points that extended past end of ideogram in circ
... You might have to give a bit more details about your code, package used, example, ... This is not enough to allow us to help you. ...
written 5 days ago by VHahaut990
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Comment: C: range of fold change in RNA seq
... Have they been sequenced at the same time? Are the coverages roughly similar (size factors?) ? ...
written 10 days ago by VHahaut990
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Comment: C: Stack several manhattan plots
... Using the facet_wrap you'll split your graph in as many chromosome as you have: library(dplyr) library(ggplot2) tmp <- data_frame( CHR=paste0("chr", sample(1:10, 1000, replace=T)), POS=seq(1,1000), pval1=1/runif(n = 1000, min=0, max=0.2), pval2=1/c(runif( ...
written 12 days ago by VHahaut990
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Answer: A: Stack several manhattan plots
... With a bit of customization you could do it in R with ggplot: library(dplyr) library(ggplot2) tmp <- data_frame( POS=seq(1,10000), pval1=1/runif(n = 10000, min=0, max=0.2), pval2=1/c(runif(n = 9999, min=0, max=0.2), 1e-5), pval3=1/runif(n = 10000, min=0, ...
written 12 days ago by VHahaut990
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Answer: C: data frame from deseq2
... Ok so you mean you want to save it as a text file somewhere? write.table(assay(rld[res.index,]), sep="\t", path, row.names=F, quote=F) where `path` should be replaced by the full path where you want to save it such as: write.table(assay(rld[res.index,]), sep="\t", "~/Desktop/rld_norma ...
written 24 days ago by VHahaut990
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Comment: C: data frame from deseq2
... Do you mean the rld normalized count table? assay(rld[res.index,] ...
written 25 days ago by VHahaut990
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Answer: A: miRNA corresponds to multiple ensembl gene IDs
... There are all paralogues: [http://www.ensembl.org/Homo_sapiens/Gene/Compara_Paralog?db=core;g=ENSG00000284332;r=1:30366-30503;t=ENST00000607096][1] [1]: http://www.ensembl.org/Homo_sapiens/Gene/Compara_Paralog?db=core;g=ENSG00000284332;r=1:30366-30503;t=ENST00000607096 ...
written 26 days ago by VHahaut990
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Answer: C: Is there an R function that transforms a decimal SAM FLAG into a list of strings
... [https://www.rdocumentation.org/packages/Rsamtools/versions/1.24.0/topics/ScanBamParam][1] This doesn't answer 100% your question but ScanBamParam() / ScanBamFlag can parse a SAM file and extract reads with certain features (isProperPair, isPaired, ...) [1]: https://www.rdocumentation.org/packa ...
written 29 days ago by VHahaut990
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Comment: C: DeconstructSigs - Multiple sample size(~90 samples)
... write.table(results, "/path/to/your/file.txt", sep="\t", quote=F, row.names=F) ...
written 4 weeks ago by VHahaut990
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Answer: A: DeconstructSigs - Multiple sample size(~90 samples)
... 1. Create a vector with your sample IDs: ids <- c("ID1", "ID2", ... , "IDn") NB: This can maybe be obtained elsewhere. If you have a dataframe that contain all the IDs in one column you could load this dataframe and extract the IDs: data <- read.table("file", sep="\t", header=T) ...
written 4 weeks ago by VHahaut990

Latest awards to VHahaut

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Scholar 12 days ago, created an answer that has been accepted. For A: miRNA corresponds to multiple ensembl gene IDs
Popular Question 21 days ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Scholar 26 days ago, created an answer that has been accepted. For A: miRNA corresponds to multiple ensembl gene IDs
Popular Question 6 weeks ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Centurion 7 weeks ago, created 100 posts.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Is it normal to have low expression levels of house keeping genes in plant RNA-s
Appreciated 5 months ago, created a post with more than 5 votes. For C: Is going back to the wet lab worth it?
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For C: Is going back to the wet lab worth it?
Appreciated 9 months ago, created a post with more than 5 votes. For C: Is going back to the wet lab worth it?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Popular Question 12 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Student 13 months ago, asked a question with at least 3 up-votes. For MA plots DESeq: strange MA plots
Supporter 13 months ago, voted at least 25 times.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Popular Question 17 months ago, created a question with more than 1,000 views. For DESeq2 analysis: huge number of outliers and refitting
Student 2.3 years ago, asked a question with at least 3 up-votes. For MA plots DESeq: strange MA plots

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