Moderator: ATpoint
ATpoint ♦ 44k
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Posts by ATpoint
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Comment:
C: Heatmaps by pheatmap
... https://stackoverflow.com/questions/36852101/r-legend-title-or-units-when-using-pheatmap ...
written 7 hours ago by
ATpoint ♦ 44k
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... I would rather find out why there is a discrepancy between the chromsizes and the wig file. You are sure it is mm9 and not mm10? The error indicates a problem and just ignoring it would probably be not so smart. In the worst case you are using the wrong reference genome. ...
written 11 hours ago by
ATpoint ♦ 44k
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... The link is broken. ...
written 14 hours ago by
ATpoint ♦ 44k
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... This filter has defaults that apply if you do not set a value. The only important thing is that you either give it `group` or the design matrix so it is aware of your design. ...
written 1 day ago by
ATpoint ♦ 44k
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... Make your life easy and use the `edgeR` filtering function `filterByExpr` which automates this process.
Why is FDR >>> p-value, yes because the multiple testing burden is large when testing thousands of genes. ...
written 1 day ago by
ATpoint ♦ 44k
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... That'd explain things. I am on
$ bash --version
GNU bash, version 3.2.57(1)-release (x86_64-apple-darwin18)
Copyright (C) 2007 Free Software Foundation, Inc.
What do you use https://www.biostars.org/u/41677/ ? ...
written 1 day ago by
ATpoint ♦ 44k
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... https://www.biostars.org/u/41677/ I suggest that instead of multiple posts with sparse content you make one single post, add your scripts, with usage information. ...
written 1 day ago by
ATpoint ♦ 44k
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... I still get the above error. ...
written 1 day ago by
ATpoint ♦ 44k
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... Hey, thanks for contributing. I would suggest though to add some documentation and confirm it works properly on Mac and Linux.
On Mac:
./foo.sh SRR5454413
./foo.sh: line 18: syntax error near unexpected token `&'
./foo.sh: line 18: ` then echo "Temp file download successful" |&a ...
written 1 day ago by
ATpoint ♦ 44k
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... By today for DESeq2 it would be the `lfcShrink` option that explicitely shrinks the logFC estimates, so you could have a look at that. Filtering by p-values is generally difficult as genes with higher expression levels have higher power and therefore generally lower p-values which is not strictly co ...
written 1 day ago by
ATpoint ♦ 44k
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For C: Does BWA mem work with uBAM file?
Teacher
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For A: Get sequence by genomic coordinates in R
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For A: What is the best way to update a list of deprecated gene symbols? (GeCKO v2 gRNA
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For A: What is the best way to update a list of deprecated gene symbols? (GeCKO v2 gRNA
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For Using EnrichedHeatmap for visualization of NGS experiments
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For A: Get sequence by genomic coordinates in R
Scholar
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For C: scaling difference between prcomp() and pcatools
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For C: How to justify the proteins by their pathways in the discussion for research pap
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For C: Does BWA mem work with uBAM file?
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For A: Get sequence by genomic coordinates in R
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For A: Get sequence by genomic coordinates in R
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For C: Does BWA mem work with uBAM file?
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For C: Does BWA mem work with uBAM file?
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24 days ago,
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For C: Does BWA mem work with uBAM file?
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27 days ago,
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For A: Get sequence by genomic coordinates in R
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For C: Does BWA mem work with uBAM file?
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