Moderator: ATpoint

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ATpoint44k
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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 ATpoint44k
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Comment: C: WIG TO BIGWIG - UCSC SOFTWARE - ERROR IN "ITEM ENDS". <URGENT>
... 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 ATpoint44k
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Comment: C: RNAseq data for Deseq2 from different library
... The link is broken. ...
written 14 hours ago by ATpoint44k
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Comment: C: Am I unnecessarily 'missing' a high number of true-positive DE genes? Or do I ju
... 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 ATpoint44k
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Comment: C: Am I unnecessarily 'missing' a high number of true-positive DE genes? Or do I ju
... 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 ATpoint44k
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Comment: C: Script: Downloading fastq files from ENA database
... 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 ATpoint44k
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Comment: C: Script: Getting information about SRX experiment ID from NCBI database
... 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 ATpoint44k
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Comment: C: Script: Downloading fastq files from ENA database
... I still get the above error. ...
written 1 day ago by ATpoint44k
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Comment: C: Script: Downloading fastq files from ENA database
... 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 ATpoint44k
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Comment: C: Expression thresholds for enrichment analysis of RNA-Seq data
... 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 ATpoint44k

Latest awards to ATpoint

Teacher 3 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Appreciated 7 days ago, created a post with more than 5 votes. For Using EnrichedHeatmap for visualization of NGS experiments
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Scholar 8 days ago, created an answer that has been accepted. For C: scaling difference between prcomp() and pcatools
Teacher 12 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 13 days ago, created an answer that has been accepted. For C: scaling difference between prcomp() and pcatools
Good Answer 13 days ago, created an answer that was upvoted at least 5 times. For A: Get sequence by genomic coordinates in R
Appreciated 13 days ago, created a post with more than 5 votes. For A: Get sequence by genomic coordinates in R
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Scholar 16 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 20 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Good Answer 21 days ago, created an answer that was upvoted at least 5 times. For A: Get sequence by genomic coordinates in R
Scholar 21 days ago, created an answer that has been accepted. For C: scaling difference between prcomp() and pcatools
Teacher 23 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 23 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 24 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 24 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Get sequence by genomic coordinates in R
Scholar 27 days ago, created an answer that has been accepted. For C: scaling difference between prcomp() and pcatools
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?

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