User: Charles Plessy

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Charles Plessy2.2k
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Japan
Website:
http://population-tran...
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Joined:
3 years, 1 month ago
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Posts by Charles Plessy

<prev • 233 results • page 1 of 24 • next >
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Comment: C: Transform a GTF file into a data frame in R
... Can you transform your comment into a formal answer, by clicking on "moderate" and selecting the appropriate option, so that cristian can "accept" the answer ? This will make the information clearer for the future readers ! ...
written 6 days ago by Charles Plessy2.2k
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Comment: C: Renaming All Files In A Directory With A Perl Script
... By the way, on Debian system (and probably Unbuntu too), Perl's `rename` command is being moved to the `rename` package. In future releases (Buster, ...) [the `perl` package will not provide the `rename` command anymore](https://bugs.debian.org/735134). ...
written 12 days ago by Charles Plessy2.2k
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Comment: C: Genome Browser suggestions
... It's work in progress. At the moment you would need to contact the browser admin. ...
written 21 days ago by Charles Plessy2.2k
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Answer: A: Genome Browser suggestions
... How about [ZENBU](http://fantom.gsc.riken.jp/zenbu) ? Here is an example illustration that I made starting from ZENBU's SVG export. ![](http://population-transcriptomics.org/images/CAGEscan.png) ...
written 24 days ago by Charles Plessy2.2k
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Answer: A: How to save GRanges object to csv file
... Using R >= 3.3.3 and Bioconductor >= 3.4, the commands that you provided worked on my computer. If you are using older versions, perhaps you can consider upgrading? > library(Homo.sapiens) > l <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene) > write.csv(l, file = "MyData.csv") > sy ...
written 24 days ago by Charles Plessy2.2k
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Answer: A: Find gene using nucleotide sequence position in R
... Here is an internal function that I am about to add to Bioconductor's [CAGEr package](https://bioconductor.org/packages/CAGEr), to solve the same problem. #' ranges2genes #' #' Assign gene symbol(s) to Genomic Ranges. #' #' @param ranges Genomics Ranges object, for example extracted from a #' ...
written 29 days ago by Charles Plessy2.2k
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Comment: C: Why is there a star in some primer sequences (library preparation)
... Just for the sake of completion, here is the quote from the manuscript: > 256 we modified each of the iTru primer sequences by adding a phosphorothioate bond > 257 (Eckstein 1985) before the 3’ nucleotide of each sequence to inhibit degradation due to the > 258 exonuclease acti ...
written 6 weeks ago by Charles Plessy2.2k
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Answer: A: Visualising indexed and sorted bam files
... You can upload the BAM files to the [ZENBU genome browser](http://fantom.gsc.riken.jp/zenbu/), that provides various ways to visualise the alignments. If you want to better see the pairing relationships, you can also convert the files to the BED12 format (see ), for which ZENBU also has good suppor ...
written 6 weeks ago by Charles Plessy2.2k
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Answer: A: counting ERCCs spike-ins in RNAseq data
... You can filter out and count the spike sequences (and rRNA, and linker) before alingment with [TagDust 2](http://tagdust.sourceforge.net/). In the following [document on GitHub](https://github.com/Population-Transcriptomics/Cell-Cycle-on-C1/blob/master/control-sequences/control-sequences.md), I used ...
written 6 weeks ago by Charles Plessy2.2k
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Answer: A: NCBI: dowload all genomes obtained from soil/marine/host associated bacteria/org
... Once you have the name or identifiers of the species you want to download, have a look at the following discussion: . ...
written 6 weeks ago by Charles Plessy2.2k

Latest awards to Charles Plessy

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 12 weeks ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 12 weeks 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
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Appreciated 3 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
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
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: why does this pipe work
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Scholar 5 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Scholar 5 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Appreciated 5 months ago, created a post with more than 5 votes. 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
Appreciated 5 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 5 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Appreciated 6 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 6 months ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Appreciated 7 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
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

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