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: 10.1093/bioinformatics/btw777

https://doi.org/10.1093/bioinformatics/btw777

Cited by: 1,059
Author(s): Davis J. McCarthy, Kieran R Campbell, Aaron T. L. Lun, Quin F. Wills
Published: over 7 years ago

Software Mentions 14

bioconductor: Biobase
Biobase: Base functions for Bioconductor
Papers that mentioned: 104
bioconductor: BiocGenerics
S4 generic functions used in Bioconductor
Papers that mentioned: 15
bioconductor: destiny
Creates diffusion maps
Papers that mentioned: 18
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: RUVSeq
Remove Unwanted Variation from RNA-Seq Data
Papers that mentioned: 91
bioconductor: scater
Single-Cell Analysis Toolkit for Gene Expression Data in R
Papers that mentioned: 79
bioconductor: scran
Methods for Single-Cell RNA-Seq Data Analysis
Papers that mentioned: 113
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
cran: Rtsne
T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
Papers that mentioned: 255
pypi: destiny

Papers that mentioned: 18
pypi: HTSeq
A framework to process and analyze data from high-throughput sequencing (HTS) assays
Papers that mentioned: 3,071
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: plot
A matplotlib frontend executable using JSON file as user input
Papers that mentioned: 63