Data

Tools

Indexes

Applications

Experiments

Papers

Papers: 10.1371/journal.pcbi.1006242

https://doi.org/10.1371/journal.pcbi.1006242

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization

Cited by: 29
Author(s): Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard
Published: about 8 years ago

Software Mentions 27

bioconductor: ggtree
an R package for visualization of tree and annotation data
Papers that mentioned: 474
Very Likely Science (100)
bioconductor: phyloseq
Handling and analysis of high-throughput microbiome census data
Papers that mentioned: 1,702
Very Likely Science (75)
bioconductor: qvalue
Q-value estimation for false discovery rate control
Papers that mentioned: 248
Very Likely Science (100)
bioconductor: SRAdb
A compilation of metadata from NCBI SRA and tools
Papers that mentioned: 20
Very Likely Science (100)
cran: ape
Analyses of Phylogenetics and Evolution
Papers that mentioned: 918
Very Likely Science (100)
cran: dplyr
A Grammar of Data Manipulation
Papers that mentioned: 1,213
Very Likely Science (100)
cran: fitdistrplus
Help to Fit of a Parametric Distribution to Non-Censored or Censored Data
Papers that mentioned: 120
Very Likely Science (91)
cran: geiger
Analysis of Evolutionary Diversification
Papers that mentioned: 179
Very Likely Science (93)
cran: gridExtra
Miscellaneous Functions for "Grid" Graphics
Papers that mentioned: 298
Very Likely Science (85)
cran: knitr
A General-Purpose Package for Dynamic Report Generation in R
Papers that mentioned: 157
Very Likely Science (75)
cran: magrittr
A Forward-Pipe Operator for R
Papers that mentioned: 107
Very Likely Science (100)
cran: MASS
Support Functions and Datasets for Venables and Ripley's MASS
Papers that mentioned: 2,353
Very Likely Science (100)
cran: MCMCpack
Markov Chain Monte Carlo (MCMC) Package
Papers that mentioned: 40
Very Likely Science (83)
cran: nlme
Linear and Nonlinear Mixed Effects Models
Papers that mentioned: 3,265
Very Likely Science (100)
cran: pbapply
Adding Progress Bar to '*apply' Functions
Papers that mentioned: 3
Very Likely Science (75)
cran: phylolm
Phylogenetic Linear Regression
Papers that mentioned: 47
Very Likely Science (100)
cran: phytools
Phylogenetic Tools for Comparative Biology (and Other Things)
Papers that mentioned: 586
Very Likely Science (100)
cran: rentrez
'Entrez' in R
Papers that mentioned: 36
Very Likely Science (75)
cran: truncnorm
Truncated Normal Distribution
Papers that mentioned: 9
Very Likely Science (75)
cran: XML
Tools for Parsing and Generating XML Within R and S-Plus
Papers that mentioned: 60
Very Likely Science (75)
pypi: ape
A Productive Environment - make/rake/ant/fab-like system with support for FOSD
Papers that mentioned: 918
Very Likely Science (65)
pypi: compiler
A data integrity check library
Papers that mentioned: 5
Very Likely Science (65)
pypi: data
Work with unicode/non-unicode data from files or strings uniformly.
Papers that mentioned: 33
Very Likely Science (65)
pypi: geiger
A radiation detection utility package
Papers that mentioned: 179
Very Likely Science (60)
pypi: parallel
Elementary parallel programming for Python
Papers that mentioned: 41
Very Likely Science (65)
pypi: phytools
Useful tools for physicists.
Papers that mentioned: 586
Very Likely Science (80)
pypi: table
Two-dimensional tables backed by Numpy with named rows and columns.
Papers that mentioned: 48
Very Likely Science (65)