User: Charles Plessy

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Charles Plessy2.4k
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Molecular biologist, open scientist and Debian developer.

Posts by Charles Plessy

<prev • 271 results • page 2 of 28 • next >
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Answer: A: Where to download older version of R packages in Bioconductor?
... Some Bioconductor packages are [redistributed by Debian](https://packages.debian.org/r-bioc-), and with a bit of luck some previous versions might be found in our [snapshot archive](http://snapshot.debian.org). ...
written 9 weeks ago by Charles Plessy2.4k
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Mappability tracks for mm10 ?
... Is there somewhere a mappability track for GRCm38/mm10 and GRCh38/hg38 [like the ones provided by ENCODE for older versions of these genomes](http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability) ? ...
mappability written 9 weeks ago by Charles Plessy2.4k
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Answer: A: Visualizing Replicates Genome Browser
... The [ZENBU](http://fantom.gsc.riken.jp/zenbu/) genome browser allows you to group samples that have common metadata and visualise their expression levels as barplots with error bars. For example, visit the following [view](http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=jNGc9CuWNFAk0fgiS_lEE): it d ...
written 9 weeks ago by Charles Plessy2.4k
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Comment: C: How to estimate the minimal amount of sequencing required for a biomarker analys
... Thanks a lot Erik, so said differently, it looks like I would (for instance) need at least 100 counts if I want to be at least 95% sure that a *E / L* ratio of 0.58 really indicates that *E > L*. > sapply(1:10 * 10, function(n) binom.test(c(n/2, n/2), p=0.5, alternative = "l")$conf.int) % ...
written 9 weeks ago by Charles Plessy2.4k
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Comment: C: Can loess.normalization be used for normalizing RNASeq performed with two ERCC m
... Not sure about the answer, but maybe you can find a hint at ? ...
written 9 weeks ago by Charles Plessy2.4k
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Answer: A: Can anyone suggest a RShiny app for displaying RNA-seq results online
... How about iDEP ? It has nice [documentation](https://idepsite.wordpress.com/) and [manucript](http://biorxiv.org/content/biorxiv/early/2017/06/09/148411.full.pdf). It offers heatmap, k-means, PCA, differential expression analysis, pathway analysis, biclustering, and more. ...
written 9 weeks ago by Charles Plessy2.4k
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Comment: C: How to estimate the minimal amount of sequencing required for a biomarker analys
... We are using CAGE ([Cap Analysis Gene Expression](https://en.wikipedia.org/wiki/Cap_analysis_gene_expression)) libraries of virus-infected cells, and the genomic intervals are viral promoters. (And yes, targeted enrichement is also planned, but that is a different story.) ...
written 9 weeks ago by Charles Plessy2.4k
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How to estimate the minimal amount of sequencing required for a biomarker analysis ?
... I have two genomic intervals, let's call them *Early* and *Late*, and their activity is measured in raw counts in quantitative sequencing experiments; let's call these numbers *E* and *L*. In some kind of biomarker analysis, am interested to know when *E > L* and when *E > 3L*. Obviously, th ...
biomarker statistics written 9 weeks ago by Charles Plessy2.4k • updated 9 weeks ago by Erik Arner20
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Answer: A: awk one line command
... To split the BED file in multiple files, with a single `awk` command, without for loops: $ cat toto.bed chr1 1 2 chr1 1 3 chr2 1 4 chr3 4 5 $ awk ' NR == FNR {chr[$1] ; next} {for (c in chr) { if ($1 == c) { print >> c".bed" close(c".bed") next }}}' toto.bed t ...
written 9 weeks ago by Charles Plessy2.4k
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Comment: C: Recommendations of Linux distros for beginners in bioinformatics
... Indeed, I have not used Ubuntu for ages, but my current experience with GNOME3, the default desktop in Debian, is that it is very simple to use. And at conferences, I plug my Debian laptop to the VGA and HDMI connector, and it Just Works, as it should with any OS. Lastly, importantly for the novic ...
written 10 weeks ago by Charles Plessy2.4k

Latest awards to Charles Plessy

Popular Question 23 days ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 3 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 7 months ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 7 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Appreciated 8 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 8 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: why does this pipe work
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Scholar 10 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Scholar 10 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Appreciated 10 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Appreciated 10 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 10 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Appreciated 11 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice

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