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.pone.0188873

https://doi.org/10.1371/journal.pone.0188873

A comprehensive analysis of breast cancer microbiota and host gene expression

Cited by: 105
Author(s): Kevin J. Thompson, James N. Ingle, Xiaojia Tang, Nicholas Chia, Patricio Jeraldo, Marina Walther-Antonio, Karunya K. Kandimalla, Stephen Johnson, Jingwen Yao, Sean C. Harrington, Vera J. Suman, Liewei Wang, Richard Weinshilboum, Judy C. Boughey, Jean Pierre A. Kocher, Heidi Nelson, Matthew P. Goetz, Krishna R. Kalari
Published: about 7 years ago

Software Mentions 11

bioconductor: BUS
Gene network reconstruction
Papers that mentioned: 4
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: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: metagenomeSeq
Statistical analysis for sparse high-throughput sequencing
Papers that mentioned: 169
bioconductor: sva
Surrogate Variable Analysis
Papers that mentioned: 511
cran: epade
Easy Plots
Papers that mentioned: 4
cran: HiveR
2D and 3D Hive Plots for R
Papers that mentioned: 5
cran: NbClust
Determining the Best Number of Clusters in a Data Set
Papers that mentioned: 181
pypi: HTSeq
A framework to process and analyze data from high-throughput sequencing (HTS) assays
Papers that mentioned: 3,071
pypi: TopHat
TopHat Platform
Papers that mentioned: 5,017