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 • 281 results • page 2 of 29 • next >
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Comment: C: suggestions to compare gene counts
... You have only one file, but with it, you generated multiple expression tables. Have you tried to compare the expression tables using software for differential gene expression ? ...
written 7 months ago by Charles Plessy2.5k
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Answer: A: suggestions to compare gene counts
... The field of [differential expression analysis](https://en.wikipedia.org/wiki/Gene_expression_profiling) is quite mature now, so I recommend to first look at existing solutions, that are based on one or two decades of experience. In case you do not know where to start and you are fine using [R](htt ...
written 7 months ago by Charles Plessy2.5k
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Answer: A: install genewise (wise2.4.1) on linux
... The `INSTALL` files states (edited for brevity): In the existing tar ball go: - make all in src directory - cd into dyc go make dyc - on linux this will fail. Then go make linux Now go: - copy dyc somewhere on your path; setenv WISECONFIGDIR to $wise-cvs-home/wi ...
written 7 months ago by Charles Plessy2.5k
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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 8 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 8 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 8 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 9 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 9 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 9 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 9 months ago by Charles Plessy2.5k

Latest awards to Charles Plessy

Scholar 10 weeks ago, created an answer that has been accepted. For A: Map human cell line RNA-seq data to virus
Scholar 10 weeks ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Parsing GENCODE GTF to simpler BED files: am I reinventing the wheel ?
Popular Question 4 months ago, created a question with more than 1,000 views. For Parsing GENCODE GTF to simpler BED files: am I reinventing the wheel ?
Popular Question 5 months 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 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 8 months ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 10 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
Popular Question 14 months ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 15 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Appreciated 15 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 15 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: why does this pipe work
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Scholar 17 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 17 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes

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