User: Philippe

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Philippe1.9k
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Posts by Philippe

<prev • 72 results • page 1 of 8 • next >
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Comment: C: Correlated/Coexpressed genes , given the name of a gene.
... Could you share your code to see why it is very slow? I gave it a try on my computer with a toy example (20'000 rows and 1'000 columns) and it only took few seconds. You should be able to do this without any problem in R. ...
written 4.5 years ago by Philippe1.9k
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Answer: A: Function for barplot
... I see several problems there (in addition to not explicitly telling us what goes wrong or providing an error message): you reassign args[i] within the loop, that might create some confusion. You better use a local variable to store the content of your file Using for (i in args) will assign the c ...
written 4.8 years ago by Philippe1.9k
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Answer: A: How to extract the longest isoform from multi fasta file
... A small script using the seqinr library in R. Maybe not the most straightforward but I wrote this quickly.   # Loading library seqinr library(seqinr) # Loading your input file fa <- read.fasta("input.fa") # Getting sequences and gene names from fa object genes <- sapply(strsplit(names(fa) ...
written 5.1 years ago by Philippe1.9k
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Comment: C: Getting Human Chimpanzee Divergent Sites
... Thanks but it does not seem I can make use of such data, at least not directly. If there is nothing preprocessed I could consider trying to extract information from those alignments. ...
written 6.2 years ago by Philippe1.9k
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Getting Human Chimpanzee Divergent Sites
... Hello everybody, I want to analyse the divergent sites between human and chimpanzee genomes. As this has been extensively studied I was expecting to easily find this information in biological databases such as UCSC genome browser or Ensembl. I found a UCSC table called ChimpSimpleDiff but it seems ...
evolution genomics comparative written 6.2 years ago by Philippe1.9k • updated 6.2 years ago by Pierre Lindenbaum122k
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Answer: A: Table 'N-Reads=F(Duplicate,Sample) ' How Can I Visualize This ?
... Hi Pierre, I had a quick look at your data and the problem seems to be its distribution (most values are 0 or close to 0, some are very high). Using a log transformation will help you even if in your case there is still a big peak of values with low values. plot(density(log2(M + 1))) Note: I use ...
written 6.2 years ago by Philippe1.9k
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Comment: C: Extract Cg Dinucleotides Coordinates From (Human) Genome
... Thanks for the code Pierre. I coded something similar (in python) but I was more interested in published solution as a comparison. ...
written 6.4 years ago by Philippe1.9k
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Extract Cg Dinucleotides Coordinates From (Human) Genome
... Hi everybody, to perform some analyses I need to extract the coordinates of all CG dinucleotides from the human genome (hg19). It would not be extremely difficult to write such a script but, for several reasons, I would prefer to rely on already existing tools or processed datasets. However, I was ...
genome written 6.4 years ago by Philippe1.9k • updated 2.6 years ago by Shicheng Guo7.7k
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Comment: C: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
... I agree with Jeremy and Larry that the initial drive to have more efficient and cheaper sequencing technologies was the HGP and the competition of Craig Venter (glad to hear some insights from people that were actually there). But I still think that, even though they are associated of this willingne ...
written 7.4 years ago by Philippe1.9k
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Answer: A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
... Hi, to my opinion here are some factors that contributed to decrease sequencing costs (some were already mentioned). Note that not all points can be applied to all technologies. Parallelization of sequencing reactions. Technologies such as Illumina, IonTorrent or Nanopore use technologies that can ...
written 7.4 years ago by Philippe1.9k

Latest awards to Philippe

Popular Question 4.5 years ago, created a question with more than 1,000 views. For Extract Cg Dinucleotides Coordinates From (Human) Genome
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Positive Selection Of Multiple Copies Of A Gene Within The Same Genome
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Which Bioinformatician Do You Follow On Twitter
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: Lightweight Structure Viewer, Callable From Linux Command Line
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Getting Human Chimpanzee Divergent Sites
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: How Do Biologists Use Inferred Phylogenies?
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: Lightweight Structure Viewer, Callable From Linux Command Line
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: Detecting Polyploidy Using An Assembly
Good Answer 5.8 years ago, created an answer that was upvoted at least 5 times. For A: How To Predict Pseudogenes In A Genome
Good Answer 5.8 years ago, created an answer that was upvoted at least 5 times. For A: Depth Of Knowledge Required To Become Expert In Ngs Bioinformatics?
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: Best Graphics Gallery Or Blogs For Bioinformatics Use
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: Can The Wget Command Be Used To Download Pdbs
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: Rna Seq Mrna|Gene Count Data Filteration
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: How To Predict Pseudogenes In A Genome
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: Where Can I Download Full Genome Sequences?
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: Plotting Density Of Snps On Chromosomes
Good Answer 5.8 years ago, created an answer that was upvoted at least 5 times. For A: Do Rpkm / Fpkm Follow Normal Distribution And Can I Run Microarray Stats On Them
Good Answer 5.8 years ago, created an answer that was upvoted at least 5 times. For A: Lightweight Structure Viewer, Callable From Linux Command Line
Good Answer 5.8 years ago, created an answer that was upvoted at least 5 times. For A: Where Can I Download Full Genome Sequences?
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: Depth Of Knowledge Required To Become Expert In Ngs Bioinformatics?
Good Answer 5.8 years ago, created an answer that was upvoted at least 5 times. For A: Rna Seq Mrna|Gene Count Data Filteration
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: Why Has The Cost Of Genome Sequencing Decline So Rapidly?

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