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/s12859-015-0763-1

https://doi.org/10.1186/s12859-015-0763-1

ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data

Cited by: 29
Author(s): Ivana Ihnatová, Eva Budínská
Published: about 9 years ago

Software Mentions 12

bioconductor: clipper
Gene Set Analysis Exploiting Pathway Topology
Papers that mentioned: 8
bioconductor: DEGraph
Two-sample tests on a graph
Papers that mentioned: 15
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: graph
graph: A package to handle graph data structures
Papers that mentioned: 45
bioconductor: graphite
GRAPH Interaction from pathway Topological Environment
Papers that mentioned: 30
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Papers that mentioned: 155
cran: gRbase
A Package for Graphical Modelling in R
Papers that mentioned: 3
pypi: clipper
A set of scripts for calling peaks on CLIP-seq data
Papers that mentioned: 8
pypi: graph
Directed and undirected graph data structures and algorithms.
Papers that mentioned: 45
pypi: graphite
Papers that mentioned: 30
pypi: Pathway
Pathway is a data processing framework which takes care of streaming data updates for you.
Papers that mentioned: 827