Moderator: Jean-Karim Heriche

Reputation:
19,560
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Location:
EMBL Heidelberg, Germany
Website:
http://jkh1.github.io/
Last seen:
14 hours ago
Joined:
7 years, 12 months ago
Email:
h******@embl.de

Posts by Jean-Karim Heriche

<prev • 2,339 results • page 2 of 234 • next >
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Comment: C: How to prove novel organism by sequencing
... I don't think there's a fixed list of criteria. I would suggest you look at the literature (e.g. search PubMed with keywords 'new species' and algae) to see what current practice is in this domain. ...
written 8 days ago by Jean-Karim Heriche20k
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Answer: A: graph for PC
... Read the docs. bg sets the background color of the points, To set the point color, use col. ...
written 8 days ago by Jean-Karim Heriche20k
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Answer: A: Any way to clustering mixed data types in microarray data and render them with 3
... First, read the docs of the functions you're using. hclust() does hierarchical clustering which means it produces a tree, not individual clusters. To get these, you need to cut the tree (check ?cutree). Second, you don't need to wrap a function in another function if you're not somehow modifying i ...
written 8 days ago by Jean-Karim Heriche20k
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Comment: C: Is there a maximum length in EMBOSS needle?
... Check that you don't have any error in your command/code (maybe show it). Another possibility is you may be running out of memory. ...
written 9 days ago by Jean-Karim Heriche20k
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Comment: C: When a chi-square value is indicating a genotyping error rather than segregation
... I think you misunderstand what a statistical hypothesis test and a p-value are. They inform you on the likelihood of observing this or more extreme data assuming that the null hypothesis is true (i.e. usually that there is no difference between what's being compared). This says nothing about the und ...
written 10 days ago by Jean-Karim Heriche20k
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Answer: C: A database to find out which genes are expressed in which cell type of origin fo
... The Gene Expression Atlas does have expression data by at least tissue type. It also includes the [tissue data from the Human Protein Atlas][1]. It's not that intuitive to navigate but if on the home page you select for example human as species and pancreas as biological condition, the search result ...
written 12 days ago by Jean-Karim Heriche20k
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Comment: C: R package for Unifrac and Weighted Unifrac other than Phyloseq?
... I don't know of another R package that has this and if there isn't any either you can code it yourself or you can use the existing implementation. To help with the latter I gave you the link to the phyloseq tutorial part on how to convert various R data structures into phyloseq objects. ...
written 13 days ago by Jean-Karim Heriche20k
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Answer: A: Is it theoretically possible to text mine symptoms following chemical exposure?
... There's plenty of text mining done in the biomedical domain on all kinds of subjects so it's possible. There's plenty of literature on the subject of text mining as well as online tutorials so do your research. As for tools to get started, check for example [Python's NLTK][1] or the [R tm package][2 ...
written 14 days ago by Jean-Karim Heriche20k
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Comment: C: R package for Unifrac and Weighted Unifrac other than Phyloseq?
... If you can get the data into R, [you can import it into phyloseq][1]. [1]: https://joey711.github.io/phyloseq/import-data.html#phyloseq-ize_data_already_in_r ...
written 14 days ago by Jean-Karim Heriche20k
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Comment: C: Validating Results from NMF Clustering & Consensus clustering
... As mentioned by Kevin, there are many ways of scoring the quality of a clustering result and none is perfect as they generally make some assumptions about either the structure of the data and/or what a good clustering should be. In many cases, what represents a good value for the score is not always ...
written 17 days ago by Jean-Karim Heriche20k

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