Moderator: Manu Prestat

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Manu Prestat3.9k
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Check out my blog here: http://exploringlifedata.blogspot.com/

Posts by Manu Prestat

<prev • 330 results • page 1 of 33 • next >
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Answer: A: obtain AT-rich coordinates hg19
... You may find what you are looking for with adding the keyword "isochores". For example: > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4662427/ > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1457033/ Bu this is a "macro" definition ("[...] **long (>200 kb)** DNA sequences that are fairly ...
written 11 months ago by Manu Prestat3.9k
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Answer: A: how to get ko definition by using KEGG API?
... An example using the REST API and python: http://exploringlifedata.blogspot.fr/ ...
written 17 months ago by Manu Prestat3.9k
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Comment: C: Split fasta/fastq into individual fasta files (ubuntu)
... Of course, it should not be a nightmare to write a script that takes a fastq file in input, and deliver per-read fasta files in output. An issue you may encounter, depending on your filesystem I guess, is the number of inodes management. An idea could be to separate the fasta files into different fo ...
written 19 months ago by Manu Prestat3.9k
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Answer: A: Getting BLAST to give output whilst running
... Some answers here: https://www.biostars.org/p/16471/ ...
written 21 months ago by Manu Prestat3.9k
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Comment: C: Parsing the NR database
... Metazoa (Taxonomy ID: 33208) could be a good candidate for "animals". ...
written 22 months ago by Manu Prestat3.9k
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Answer: A: Metagenomics functional annotation hmmsearch vs Blast ???
... There is also this hmm db: http://cbb.pnnl.gov/portal/software/FOAM.html (for which, I should say, I was a bit involved). ...
written 24 months ago by Manu Prestat3.9k
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Comment: C: Color Triangle and plot
... Hi, well, here I've just randomly generated 400 values between 0 and 1 (such as your triangle example) for A, B and C. Instead, I believe you would make a matrix with B,C,A as columns (to be in the same order as RGB in your example), and your measurements as rows. And then you plot with pixmapRGB() ...
written 2.6 years ago by Manu Prestat3.9k
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Comment: C: Software for viewing very large data
... or zcat ;-) ...
written 2.6 years ago by Manu Prestat3.9k
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Answer: A: Color Triangle and plot
... What about pixmapRGB() ? library(pixmap) A <- runif(n = 400, min = 0, max = 1) B <- runif(n = 400, min = 0, max = 1) C <- runif(n = 400, min = 0, max = 1) z <- pixmapRGB(c(B,C,A), 20, 20, bbox=c(-1,-1,1,1)) plot(z) ...
written 2.6 years ago by Manu Prestat3.9k
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Answer: A: How to extract chrX, chrY and chrM from a vcf file?
... Using vcftools you could pass the chromosomes you want to keep (or exclude) with the position filtering option: POSITION FILTERING --chr --not-chr Includes or excludes sites with indentifiers matching . These options may be used multiple times to include or exclude more ...
written 2.6 years ago by Manu Prestat3.9k

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Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Best Python Support Vector Machine Implementation For Bioinformatics (Classifyin
Great Question 16 months ago, created a question with more than 5,000 views. For How To Filter A Blast Xml Output ?
Appreciated 22 months ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For A: Pyfasta Split By Header
Great Question 24 months ago, created a question with more than 5,000 views. For How To Concatenate/Merge Blast Xml Outputs?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Estimation Of The Probability Of Chimera In A Metagenomic Assembly?
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Appreciated 2.6 years ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Scholar 2.8 years ago, created an answer that has been accepted. For A: Show Progress (Bar?) For Blast+ Query
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Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Transition/Transversion Ratio From Fastq Files
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Appreciated 3.2 years ago, created a post with more than 5 votes. For C: Single Gene Orthologs
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How To Filter A Blast Xml Output ?
Good Answer 3.4 years ago, created an answer that was upvoted at least 5 times. For A: Calculating P-Values From Z-Scores
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