Mmuphin wrapper #6584
Mmuphin wrapper #6584
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renu-pal
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tools/mmuphin/.shed.yml
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| long_description: | | ||
| MMUPHin is a Bioconductor package implementing meta-analysis methods for microbial community profiles. It has interfaces for: a) covariate-controlled batch and study effect adjustment, b) meta-analytic differential abundance testing, and meta-analytic discovery of c) discrete (cluster-based) or d) continuous unsupervised population structure. | ||
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| Overall, MMUPHin enables the normalization and combination of multiple microbial community studies. It can then help in identifying microbes, genes, or pathways that are differential with respect to combined phenotypes. Finally, it can find clusters or gradients of sample types that reproduce consistently among studies |
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long_description is redundant here.
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long_description was duplicated in earlier code. It is completely removed now in 801cc88
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I misunderstood and removed the whole thing but made the correction later: 7fafc59
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@renu-pal Thanks for the contribution. Some of the comments inline.
Please also reduce the test-data size for this file: tools/mmuphin/test-data/CRC_abd.tsv (Ideally, the file needs to be below 1M)
tools/mmuphin/mmuphin.xml
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| library(ggplot2) | ||
| library(readr) | ||
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| source(adjust_batch.R) |
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You will also need to add adjust_batch.R script to your test-data and source that here
Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
Co-authored-by: Saim Momin <[email protected]>
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Fixed with: renu-pal#4
@SaimMomin12 there is no need to add R files to the wrapper and source them, the package provides this functions |
New to tool wrapping , so need a bit of help in finding what is wrong with this code :)