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R script to reproduce \"Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities\".

Lukas Beule
The R script and data are available for download: https://b-web.bonares.de/smartEditor/rest/upload/ID_7050_2020_05_13_Beule_Karlovsky.zip R script and data for the reproduction of the paper entitled "Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities" by Lukas Beule and Petr Karlovsky. Comparison of scaling with ranked subsampling (SRS) with rarefying for the normalization of species count data in ecology. The example provided is a library obtained from next generation sequencing of...

Scaling with ranked subsampling (SRS) algorithm for the normalization of species count data.

Lukas Beule
An implementation of SRS in R is available for download: https://b-web.bonares.de/smartEditor/rest/upload/ID_7049_2020_05_13_SRS_function_v1_0_R.zip Scaling with ranked subsampling (SRS) is an algorithm for the normalization of species count data in ecology. So far, SRS has successfully been applied to microbial community data. SRS consists of two steps. In the first step, the counts for all OTUs (operational taxonomic untis) are divided by a scaling factor chosen in such a way that the sum of the scaled counts (Cscaled...

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