Moderator: Jean-Karim Heriche
Jean-Karim Heriche ♦ 21k
- Reputation:
- 21,320
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- Location:
- EMBL Heidelberg, Germany
- Website:
- http://jkh1.github.io/
- Last seen:
- an hour ago
- Joined:
- 8 years, 7 months ago
- Email:
- h******@embl.de
Posts by Jean-Karim Heriche
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... What you're trying to do is unclear. What do you need random data for? ...
written 4 days ago by
Jean-Karim Heriche ♦ 21k
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... To address question 1, I would suggest to use the R [igraph package][1]. There's an [excellent tutorial here][2].
Starting from a binary matrix A that can be considered as the adjacency matrix of the graph, you can do something like:
library(igraph)
G <- graph_from_adjacency_matrix(A)
...
written 5 days ago by
Jean-Karim Heriche ♦ 21k
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... Dealing with large data sets has become a more common issue although it is not specific to bioinformatics. However, for bioinformatics data types, there may exist specific tools. Here we're dealing with a count matrix and although replies currently suggest generic solutions, maybe someone has a more ...
written 6 days ago by
Jean-Karim Heriche ♦ 21k
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... Two R packages that may be of interest:
- the [bigmemory package][1] and its read.big.matrix() function.
- the [ff package][2] with its read.table.ffdf() function.
[1]: https://CRAN.R-project.org/package=bigmemory
[2]: https://CRAN.R-project.org/package=ff ...
written 6 days ago by
Jean-Karim Heriche ♦ 21k
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... Yes. If you install R with conda, also install the packages with conda, don't do it from R.
EDIT: Also pay attention to which channel(s) you're using. There may be different versions of packages in different channels that may not be compatible. I'd suggest to stick to the following channels: defa ...
written 7 days ago by
Jean-Karim Heriche ♦ 21k
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... If using conda, you should use it for everything, especially where R is concerned. This means installing everything R-related with conda. In general, mixing conda and system-based installation is a recipe for problems. ...
written 7 days ago by
Jean-Karim Heriche ♦ 21k
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... s3fs has a maximum file size (which depends on the multipart_size parameter). Check that you're not exceeding this. ...
written 8 days ago by
Jean-Karim Heriche ♦ 21k
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Comment:
C: Create a heatmap
... You can combine the columns how you like as long that it makes sense. For example, averaging doesn't make much sense if the underlying distribution of the data is multimodal or heavily skewed. ...
written 9 days ago by
Jean-Karim Heriche ♦ 21k
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... For R, check the [taxonomizr package][1].
[1]: https://cran.r-project.org/package=taxonomizr ...
written 12 days ago by
Jean-Karim Heriche ♦ 21k
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... And another [related previous post][1].
[1]: https://www.biostars.org/p/304175/ ...
written 12 days ago by
Jean-Karim Heriche ♦ 21k
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