Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities
نویسندگان
چکیده
منابع مشابه
GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data
Normalization is the first critical step in microbiome sequencing data analysis used to account for variable library sizes. Current RNA-Seq based normalization methods that have been adapted for microbiome data fail to consider the unique characteristics of microbiome data, which contain a vast number of zeros due to the physical absence or under-sampling of the microbes. Normalization methods ...
متن کاملMicrobial Ecology at Sea : Sampling , Subsampling and Incubation Considerations
Thl' l1larit1l' 1'11vironll1l'nt is the largest contiguous habitat on Earth; hllwl'vl'r, it is fill' frnm bdng homogeneous. Relevant ecological time and SPdL'l' Sl'ilil's span mUrl' than nine orders of magnitude (Figure 2.1; Dickey, ll)l) 1), t!1l'l'l'by contributing to the challenge of adequate and representatin' s.lmpling uf thl~ marine environment. Man;.' distinct marine ecosystems and their...
متن کاملSubsampling scaling
In real-world applications, observations are often constrained to a small fraction of a system. Such spatial subsampling can be caused by the inaccessibility or the sheer size of the system, and cannot be overcome by longer sampling. Spatial subsampling can strongly bias inferences about a system's aggregated properties. To overcome the bias, we derive analytically a subsampling scaling framewo...
متن کاملTheoretical microbial ecology without species.
Ecosystems are commonly conceptualized as networks of interacting species. However, partitioning natural diversity of organisms into discrete units is notoriously problematic and mounting experimental evidence raises the intriguing question whether this perspective is appropriate for the microbial world. Here an alternative formalism is proposed that does not require postulating the existence o...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: PeerJ
سال: 2020
ISSN: 2167-8359
DOI: 10.7717/peerj.9593