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/s12859-021-04142-3

https://doi.org/10.1186/s12859-021-04142-3

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

Cited by: 11
Author(s): Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise A Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordóñez, Andrew E. Jaffe, Leonardo Collado‐Torres
Published: over 3 years ago

Software Mentions 13

bioconductor: clusterProfiler
A universal enrichment tool for interpreting omics data
Papers that mentioned: 2,223
bioconductor: iSEE
Interactive SummarizedExperiment Explorer
Papers that mentioned: 13
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: SummarizedExperiment
SummarizedExperiment container
Papers that mentioned: 52
cran: pheatmap
Pretty Heatmaps
Papers that mentioned: 2,572
cran: regtools
Regression and Classification Tools
Papers that mentioned: 6
pypi: Archive
Simple library that provides a common interface for extracting zip and tar archives.
Papers that mentioned: 363
pypi: conda
OS-agnostic, system-level binary package manager.
Papers that mentioned: 92
pypi: docker
A Python library for the Docker Engine API.
Papers that mentioned: 39
pypi: ensembl
Ensembl REST API Client
Papers that mentioned: 212
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: linux

Papers that mentioned: 450
pypi: regtools
High-level Regression Utilities
Papers that mentioned: 6