User: romain.lannes

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Posts by romain.lannes

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Comment: C: Help with NGS analysis
... your question is to broad. splease specify what type of ngs you do (rna-seq, genomic), and what you want to do with. ...
written 4 months ago by romain.lannes70
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Answer: A: graph theory with applications to biology/bioinformatics
... Graph theorie is begin to be use to infer homology relation. But also to study gene and genome relation ship https://www.ncbi.nlm.nih.gov/pubmed/26774999 is a review (made by lab) about this subject. Is also worth mentioning that hogenom ( a homology database host in LYON france) is done with SILIX ...
written 4 months ago by romain.lannes70
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All proteins sequences from all complete Genome from NCBI
... I wonder if is an easy way or an already existing solution to get all proteins sequences (some may be predict) from all Complete genome ( predicted or not, from cultivated and uncultivated organisms) from ncbi. ...
genome written 4 months ago by romain.lannes70
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Comment: C: FASTA sequence modification
... you could check this post for the second part of your question [multiline fasta to one line fasta][1]. for the fisrt part I find a way with sed [StackOverflow][2] sed '/^\s*$/d' file. [1]: https://www.biostars.org/p/9262/ [2]: http://stackoverflow.com/questions/10618798/removing-new-line-char ...
written 7 months ago by romain.lannes70
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Comment: C: Gene Ontology Classification GAF format
... it is may be a duplicate of https://www.biostars.org/p/181201/ ...
written 12 months ago by romain.lannes70
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RNA intra-condition paralogue expression
... Hi, I am working in the expression of duplicate gene inside a same condition (same experiment). for example does all the paralogue are express? or just several? are some more express than other? I wonder if in this case comparing set of gene inside a condition fpkm or tmp value would be sufficient ...
rna-seq written 12 months ago by romain.lannes70
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Comment: C: Cell cycle expression/ChIP in mouse
... I have recently discover to this site in which you may be found what you are looking for and at least research are easier than in geo. http://epigenomesportal.ca/ihec/index.html ...
written 13 months ago by romain.lannes70
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ChIP-seq(histon mark) comparing pairs of gene in same condition
... Hi, I have a list of pairs genes and I want to know if they are differentially enriched in a particularly histone mark in the same conditions. I made some research and it seems all actual software are design to compare a same gene in different condition. So initially I though to use the number of ...
chip-seq written 13 months ago by romain.lannes70
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Comment: C: Comparison between two sets of genes
... what are you meaning by pathways? interaction? if it is the case I suggest you to have look to the stringDB database http://string-db.org/ ...
written 13 months ago by romain.lannes70
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Comment: C: Retrieve GO terms ontology
... It is a very interresting tool thanks again ! ...
written 14 months ago by romain.lannes70

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