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.0125000

https://doi.org/10.1371/journal.pone.0125000

From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data

Cited by: 6
Author(s): Jilong Li, Jie Hou, Sun Liang, Jordan Wilkins, Yuan Lu, Chad E. Niederhuth, Benjamin Ryan Merideth, Thomas P. Mawhinney, Valeri V. Mossine, C. Michael Greenlief, John C. Walker, William R. Folk, Mark Hannink, Dennis B. Lubahn, James A. Birchler, Jianlin Cheng
Published: over 9 years ago

Software Mentions 8

bioconductor: baySeq
Empirical Bayesian analysis of patterns of differential expression in count data
Papers that mentioned: 139
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: NOISeq
Exploratory analysis and differential expression for RNA-seq data
Papers that mentioned: 321
cran: igraph
Network Analysis and Visualization
Papers that mentioned: 1,555
pypi: HTSeq
A framework to process and analyze data from high-throughput sequencing (HTS) assays
Papers that mentioned: 3,071
pypi: igraph
High performance graph data structures and algorithms
Papers that mentioned: 1,555
pypi: TopHat
TopHat Platform
Papers that mentioned: 5,017