User: benformatics

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benformatics1.1k
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ETH Zurich
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Posts by benformatics

<prev • 118 results • page 1 of 12 • next >
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Comment: C: Feature selection for differential analysis
... You should not keep the unique genes. If there is only a small number of them then you might be OK just excluding them. If it is a huge proportion of genes then what @kristoffer.vittingseerup suggested below is probably wise. ...
written 7 weeks ago by benformatics1.1k
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Answer: A: plotTracks - empty plot and custom genomes
... When I run your first block of code I am able to produce the following plot as expected (R version 3.6.0; Gviz version 1.28.0): ![gviz plot][1] [1]: http://i.ibb.co/rsYS2qP/Rplot04.png An earlier R install gave me an error: `There doesn't seem to be any cytoband data available for genome 'hg38' ...
written 8 weeks ago by benformatics1.1k
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Answer: A: Hypergeometric test of gene list overlap
... So if I get this straight. You want to see if there is an enrichment of genes from A in either B or C. Overall it looks like your setup is good. Your universe (`n`) is all the genes in across your samples. The q-value depends on the question you want to ask. In your case you seem to be making a de ...
written 9 weeks ago by benformatics1.1k
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Comment: C: Concept behind p-value correction?
... ![https://imgs.xkcd.com/comics/significant.png][1] [1]: https://imgs.xkcd.com/comics/significant.png ...
written 9 weeks ago by benformatics1.1k
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Comment: C: Convert regex into DNAString object
... What is the problem with just converting the `DNAString` to a `character` and doing your regex with that? ...
written 9 weeks ago by benformatics1.1k
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Comment: C: Make org.db dynamic in AnnotationDbi::mapIds()
... entrez_Ids <- mapIds(eval(parse(text = org_pkg)), as.character(genelist), 'ENTREZID', 'ENSEMBL') ...
written 10 weeks ago by benformatics1.1k
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Comment: C: Make org.db dynamic in AnnotationDbi::mapIds()
... Good question! library(org_pkg,character.only=TRUE) ...
written 10 weeks ago by benformatics1.1k
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Comment: C: How to sort the Q matrix from structure analyses based on countires first and th
... If you have names for your columns you can do it with those too. e.g. Q.matrix <- Q.matrix[order(Q.matrix$country,Q.matrix$Q,] ...
written 10 weeks ago by benformatics1.1k
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Answer: A: How to sort the Q matrix from structure analyses based on countires first and th
... Order by column 8 first and then "sub"-order by column 7 Q.matrix <- Q.matrix[order(Q.matrix[,8],Q.matrix[,7]),] EDIT: Actually this might be wrong... what column is Q? If it's not a variable in your data.frame it will be hard to use it for ordering. Otherwise you can split your data.fram ...
written 10 weeks ago by benformatics1.1k
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Comment: C: vcf from sorted bam
... You could try making the VCFs separately and then using GATK tools: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_GenotypeGVCFs.php https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellben ...
written 10 weeks ago by benformatics1.1k

Latest awards to benformatics

Appreciated 8 weeks ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Concept behind p-value correction?
Scholar 10 weeks ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Guru 10 weeks ago, received more than 100 upvotes.
Scholar 10 weeks ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: ATAC-seq peak calling with MACS
Centurion 11 weeks ago, created 100 posts.
Scholar 11 weeks ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Appreciated 3 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Popular Question 3 months ago, created a question with more than 1,000 views. For ".1" being appended to Ensembl Gene IDs from UCSC txdb (dm6)
Scholar 4 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 4 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Subset of genes with at least 1 intron larger than 5000 kbp
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Appreciated 7 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Scholar 7 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Scholar 7 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Supporter 7 months ago, voted at least 25 times.
Scholar 7 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb

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