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/s13059-014-0560-6

https://doi.org/10.1186/s13059-014-0560-6

Gateways to the FANTOM5 promoter level mammalian expression atlas

Cited by: 634
Author(s): Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda, Fumi Hori, Sachi Ishikawa-Kato, Christopher J. Mungall, Peter Arner, J Kenneth Baillie, Nicolas Bertin, Hidemasa Bono, Michiel de Hoon, Alexander D. Diehl, Emmanuel Dimont, Tom C. Freeman, Kaori Fujieda, Winston Hide, Rajaram Kaliyaperumal, Toshiaki Katayama, Timo Lassmann, Terrence F. Meehan, Koro Nishikata, Ono Hiromasa, Michael Rehli, Albin Sandelin, Erik Schultes, Peter A.C. ’t Hoen, Zuotian Tatum, Mark Thompson, Tetsuro Toyoda, Derek W. Wright, Carsten O. Daub, Masayoshi Itoh, Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji
Published: almost 10 years ago

Software Mentions 5

bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Papers that mentioned: 1,962
cran: JASPAR
R modules for JASPAR databases: a collection of transcription factor DNA-binding preferences, modeled as matrices
Papers that mentioned: 1,283
cran: MCL
Markov Cluster Algorithm
Papers that mentioned: 563
cran: SPARQL
SPARQL client
Papers that mentioned: 660
pypi: CAGE
A generic and fairly complete cellular automata simulation engine.
Papers that mentioned: 101