User: Charles Plessy

gravatar for Charles Plessy
Charles Plessy2.7k
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Japan
Website:
http://population-tran...
Last seen:
2 weeks ago
Joined:
4 years, 11 months ago
Email:
c***************@plessy.org

Molecular biologist, open scientist and Debian developer.

Posts by Charles Plessy

<prev • 283 results • page 2 of 29 • next >
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Comment: C: Login with identity providers: can we have an alternative to Google?
... Cool; I missed it; thank you. Closing this post accordingly. ...
written 15 months ago by Charles Plessy2.7k
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(Closed) Login with identity providers: can we have an alternative to Google?
... It was convenient to use GitHub as an identity provider. Will it have a chance to come back? Alternatively, how about GitLab or ORCID? ...
meta written 15 months ago by Charles Plessy2.7k
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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 17 months ago by Charles Plessy2.7k
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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 17 months ago by Charles Plessy2.7k
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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 17 months ago by Charles Plessy2.7k
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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 17 months ago by Charles Plessy2.7k
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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 18 months ago by Charles Plessy2.7k
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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 18 months ago by Charles Plessy2.7k
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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 18 months ago by Charles Plessy2.7k
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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 18 months ago by Charles Plessy2.7k

Latest awards to Charles Plessy

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
Popular Question 10 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 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 12 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Scholar 12 months ago, created an answer that has been accepted. For A: Map human cell line RNA-seq data to virus
Popular Question 12 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 13 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 14 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 15 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 17 months ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 20 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 2.1 years ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Appreciated 2.1 years ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 2.1 years ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: why does this pipe work

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