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.0075146

https://doi.org/10.1371/journal.pone.0075146

NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations

Cited by: 29
Author(s): Ivan Merelli, Píetro Lió, Luciano Milanesi
Published: about 11 years ago

Software Mentions 12

bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Papers that mentioned: 1,962
bioconductor: biomaRt
Interface to BioMart databases (i.e. Ensembl)
Papers that mentioned: 446
bioconductor: BSgenome
Software infrastructure for efficient representation of full genomes and their SNPs
Papers that mentioned: 47
bioconductor: GEOquery
Get data from NCBI Gene Expression Omnibus (GEO)
Papers that mentioned: 328
bioconductor: KEGGREST
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
Papers that mentioned: 75
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: Rgraphviz
Provides plotting capabilities for R graph objects
Papers that mentioned: 33
cran: ergm
Fit, Simulate and Diagnose Exponential-Family Models for Networks
Papers that mentioned: 19
cran: igraph
Network Analysis and Visualization
Papers that mentioned: 1,555
cran: SAM
Sparse Additive Modelling
Papers that mentioned: 4,566
cran: samr
SAM: Significance Analysis of Microarrays
Papers that mentioned: 114
pypi: igraph
High performance graph data structures and algorithms
Papers that mentioned: 1,555