Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Papers: 10.1371/journal.pcbi.1003531

https://doi.org/10.1371/journal.pcbi.1003531

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

Cited by: 2,083
Author(s): Paul J. McMurdie, Susan Holmes
Published: over 10 years ago

Software Mentions 17

bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
bioconductor: metagenomeSeq
Statistical analysis for sparse high-throughput sequencing
Papers that mentioned: 169
bioconductor: multtest
Resampling-based multiple hypothesis testing
Papers that mentioned: 158
bioconductor: phyloseq
Handling and analysis of high-throughput microbiome census data
Papers that mentioned: 1,702
cran: cluster
"Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al.
Papers that mentioned: 416
cran: foreach
Provides Foreach Looping Construct
Papers that mentioned: 50
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
cran: knitr
A General-Purpose Package for Dynamic Report Generation in R
Papers that mentioned: 157
cran: plyr
Tools for Splitting, Applying and Combining Data
Papers that mentioned: 468
cran: PoiClaClu
Classification and Clustering of Sequencing Data Based on a Poisson Model
Papers that mentioned: 12
cran: reshape2
Flexibly Reshape Data: A Reboot of the Reshape Package
Papers that mentioned: 421
cran: ROCR
Visualizing the Performance of Scoring Classifiers
Papers that mentioned: 596
cran: vegan
Community Ecology Package
Papers that mentioned: 6,903
pypi: cluster

Papers that mentioned: 416
pypi: plyr
UNKNOWN
Papers that mentioned: 468
pypi: stats
Calculator-style statistical functions
Papers that mentioned: 3,105