User: Charles Plessy

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Charles Plessy2.5k
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Japan
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Molecular biologist, open scientist and Debian developer.

Posts by Charles Plessy

<prev • 278 results • page 2 of 28 • next >
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Answer: A: HOw to merge multifasta sequence into a single sequence having only one header?
... Using the [union](http://emboss.sourceforge.net/apps/cvs/emboss/apps/union.html) command from the [EMBOSS](http://emboss.sourceforge.net/) package: $ cat test.fasta >seq1 AAAATTGGG >seq2 GGCCCTTTT >seq3 AAATGGGG $ union -filter test.fasta >seq1 ...
written 3 months ago by Charles Plessy2.5k
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Comment: C: How can I install xml development headers (version 2.9.1) and xz development he
... > xz development headers (version 5.1.1 tested) In doubt, you can also query the APT cache for package descriptions. $ apt search xz development files Sorting... Done Full Text Search... Done devscripts/stable,now 2.17.6+deb9u1 amd64 [installed] scripts to make the life of ...
written 4 months ago by Charles Plessy2.5k
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Answer: A: Demultiplex pair-end fastq reads with barcode 2 in the identifier line
... How about pasting your first barcode to the reads, and demultiplexing with virtual barcodes that represent all the combinations of barcode 1 and 2 ? Here is one way to paste. paste -d '' <(grep '^@' test.fq | sed s/.*:// | perl -ne 'chomp;print"\n$_\n\n","I"x(length($_)),"\n"') test.fq ...
written 4 months ago by Charles Plessy2.5k
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Comment: C: Read genomic ranges from a very big file in R
... Have a look at all the `import` commands of the [rtracklayer](https://bioconductor.org/packages/rtracklayer) package. ...
written 4 months ago by Charles Plessy2.5k
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Comment: C: extracting a column by grepping particular rows
... Do you see the same numbers when following the very good answer of cpad0112 ? ...
written 4 months ago by Charles Plessy2.5k
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Answer: A: extracting a column by grepping particular rows
... If your data is not too large, a Unix shell command may be enough: Here I create files containing your example data, assuming you really meant that it is *space-separated*. cat > counts.txt <<_END_ gene_name sample_1 sample_2 sample_3 gene_1 count_1count_1 count_1 gene_2 c ...
written 4 months ago by Charles Plessy2.5k
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Answer: A: package 'karyoploteR' is not available (for R version 3.3.3)
... The [karyotypeR page on the Bioconductor website](https://bioconductor.org/packages/release/bioc/html/karyoploteR.html) indicates that the karyotypeR package requires a version of R equal or higher to 3.4. So you would need to upgrade R (or install R >= 3.4 in parallel with your current version) ...
written 5 months ago by Charles Plessy2.5k
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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 5 months ago by Charles Plessy2.5k
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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 5 months ago by Charles Plessy2.5k
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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 5 months ago by Charles Plessy2.5k

Latest awards to Charles Plessy

Popular Question 27 days ago, created a question with more than 1,000 views. For Parsing GENCODE GTF to simpler BED files: am I reinventing the wheel ?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 3 months ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 6 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 10 months ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 11 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Appreciated 11 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 11 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: why does this pipe work
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Scholar 13 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Scholar 13 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Appreciated 13 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Appreciated 13 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 13 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes

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