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It seems to crash because of zero edges in STRING?
$ cmonkey2 --organism sce data.tsv
2017-06-06 15:16:23 INFO checking MEME...
2017-06-06 15:16:25 INFO Input matrix has # rows: 4640, # …
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I recently attempted two separate runs using microarray data from human and mouse samples.
I collected all protein network data from STRING v9.1 for use as the string files with either species, forma…
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Hello,
I am running cmonkey2 on human data. I downloaded the RSAT files for Homo_sapiens_GRCh38 and use them with the –rsat_dir, --rsat_features and –rsat_organism option.
I am using a ratio f…
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Hello,
I am Lang and want to submit XINA to Bioconductor. I checked XINA by using R CMD Check and Bioccheck and found no warnings and no errors. Of course, I know these are just minimum requirement…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/sysbiomed/glmSparseNet
Confirm the following by e…
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I have tried with no success to set up the local building test.
With circleci build, I do not seem to have gcc in the build environment. Here is an example with fastree recipe incremented by 1.
`…
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Hi,
In line 99 of stringdb.py, I think 'total_nodes += 1' should be tabbed over (so it's within the 'if not node in keep_node:' block), as currently it counts each gene more than once. (This means th…
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I tried running cmonkey2 with the example data at https://github.com/baliga-lab/cmonkey2/blob/master/example_data/hal/halo_ratios5.tsv. I am not sure why I am receiving an error. The terminal output i…
wwick updated
7 years ago
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Hello,
I just came up with a new question related to the previous problem I had.
Now I am running cMonkey on a Ecoli data table. We have the exactly same name in my String file and data table but …
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/BIMSBbioinfo/netSmooth
Confirm the following by e…