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: 10.1186/s12859-017-1994-0

https://doi.org/10.1186/s12859-017-1994-0

Cited by: 30
Author(s): Qin Zhu, Stephen Fisher, Hannah Dueck, Sarah A. Middleton, Mugdha Khaladkar, Junhyong Kim
Published: over 6 years ago

Software Mentions 15

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: monocle

Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Papers that mentioned: 60

bioconductor: SC3

Single-Cell Consensus Clustering
Papers that mentioned: 71

bioconductor: vsn

Variance stabilization and calibration for microarray data
Papers that mentioned: 91

cran: gplots

Various R Programming Tools for Plotting Data
Papers that mentioned: 2,122

cran: igraph

Network Analysis and Visualization
Papers that mentioned: 1,555

cran: networkD3

D3 JavaScript Network Graphs from R
Papers that mentioned: 37

cran: Seurat

Tools for Single Cell Genomics
Papers that mentioned: 1,512

cran: shinyAce

Ace Editor Bindings for Shiny
Papers that mentioned: 3

cran: threejs

Interactive 3D Scatter Plots, Networks and Globes
Papers that mentioned: 7

cran: visNetwork

Network Visualization using 'vis.js' Library
Papers that mentioned: 49

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: monocle

An async programming framework with a blocking look-alike syntax
Papers that mentioned: 60