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: 10.7554/eLife.43257

https://doi.org/10.7554/eLife.43257

Cited by: 65
Author(s): Yanshu Wang, Mark F Sabbagh, Xiaowu Gu, Amir Rattner, John Williams, Jeremy Nathans
Published: about 5 years ago

Software Mentions 10

bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: DiffBind
Differential Binding Analysis of ChIP-Seq Peak Data
Papers that mentioned: 217
bioconductor: EBSeq
An R package for gene and isoform differential expression analysis of RNA-seq data
Papers that mentioned: 261
bioconductor: tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Papers that mentioned: 367
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
cran: pheatmap
Pretty Heatmaps
Papers that mentioned: 2,572
cran: tidyverse
Easily Install and Load the 'Tidyverse'
Papers that mentioned: 1,023
pypi: deepTools
Useful tools for exploring deep sequencing data.
Papers that mentioned: 435
pypi: kallisto
The Kallisto software enables the efficient calculation of atomic features that can be used within a quantitative structure-activity relationship (QSAR) approach. Furthermore, several modelling helpers are implemented.
Papers that mentioned: 307
pypi: MACS2
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,203