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: 10.12688/f1000research.17824.2

https://doi.org/10.12688/f1000research.17824.2

Cited by: 2
Author(s): Michael Prummer
Published: almost 5 years ago

Software Mentions 51

bioconductor: AnnotationDbi
Manipulation of SQLite-based annotations in Bioconductor
Papers that mentioned: 73
bioconductor: BiocGenerics
S4 generic functions used in Bioconductor
Papers that mentioned: 15
bioconductor: BiocParallel
Bioconductor facilities for parallel evaluation
Papers that mentioned: 30
bioconductor: BiocWorkflowTools
Tools to aid the development of Bioconductor Workflow packages
Papers that mentioned: 2
bioconductor: CAMERA
Collection of annotation related methods for mass spectrometry data
Papers that mentioned: 429
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: EGSEA
Ensemble of Gene Set Enrichment Analyses
Papers that mentioned: 22
bioconductor: GenomeInfoDb
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Papers that mentioned: 7
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: SummarizedExperiment
SummarizedExperiment container
Papers that mentioned: 52
bioconductor: zlibbioc
An R packaged zlib-1.2.5
Papers that mentioned: 2
cran: acepack
ACE and AVAS for Selecting Multiple Regression Transformations
Papers that mentioned: 2
cran: BiocManager
Access the Bioconductor Project Package Repository
Papers that mentioned: 35
cran: caTools
Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
Papers that mentioned: 52
cran: cowplot
Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Papers that mentioned: 298
cran: dplyr
A Grammar of Data Manipulation
Papers that mentioned: 1,213
cran: GGally
Extension to 'ggplot2'
Papers that mentioned: 87
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
cran: ggrepel
Automatically Position Non-Overlapping Text Labels with 'ggplot2'
Papers that mentioned: 164
cran: gplots
Various R Programming Tools for Plotting Data
Papers that mentioned: 2,122
cran: gridExtra
Miscellaneous Functions for "Grid" Graphics
Papers that mentioned: 298
cran: GSA
Gene Set Analysis
Papers that mentioned: 285
cran: gtools
Various R Programming Tools
Papers that mentioned: 60
cran: Hmisc
Harrell Miscellaneous
Papers that mentioned: 1,000
cran: igraph
Network Analysis and Visualization
Papers that mentioned: 1,555
cran: kableExtra
Construct Complex Table with 'kable' and Pipe Syntax
Papers that mentioned: 21
cran: KernSmooth
Functions for Kernel Smoothing Supporting Wand & Jones (1995)
Papers that mentioned: 34
cran: knitr
A General-Purpose Package for Dynamic Report Generation in R
Papers that mentioned: 157
cran: lazyeval
Lazy (Non-Standard) Evaluation
Papers that mentioned: 3
cran: locfit
Local Regression, Likelihood and Density Estimation
Papers that mentioned: 35
cran: magrittr
A Forward-Pipe Operator for R
Papers that mentioned: 107
cran: matrixStats
Functions that Apply to Rows and Columns of Matrices (and to Vectors)
Papers that mentioned: 46
cran: pkgconfig
Private Configuration for 'R' Packages
Papers that mentioned: 3
cran: RColorBrewer
ColorBrewer Palettes
Papers that mentioned: 490
cran: RCurl
General Network (HTTP/FTP/...) Client Interface for R
Papers that mentioned: 36
cran: rlang
Functions for Base Types and Core R and 'Tidyverse' Features
Papers that mentioned: 16
cran: rpart
Recursive Partitioning and Regression Trees
Papers that mentioned: 431
cran: rprojroot
Finding Files in Project Subdirectories
Papers that mentioned: 1
cran: RSQLite
SQLite Interface for R
Papers that mentioned: 27
cran: SnowballC
Snowball Stemmers Based on the C 'libstemmer' UTF-8 Library
Papers that mentioned: 14
cran: tidyselect
Select from a Set of Strings
Papers that mentioned: 3
cran: tm
Text Mining Package
Papers that mentioned: 94
cran: viridisLite
Colorblind-Friendly Color Maps (Lite Version)
Papers that mentioned: 7
cran: WGCNA
Weighted Correlation Network Analysis
Papers that mentioned: 3,479
cran: wordcloud
Word Clouds
Papers that mentioned: 39
pypi: ggplot
ggplot for python
Papers that mentioned: 796
pypi: GSA
Python Package to implement Gravitational Search Algorithm. Documentation at:https://github.com/deepanshu1999/GSA
Papers that mentioned: 285
pypi: igraph
High performance graph data structures and algorithms
Papers that mentioned: 1,555
pypi: pkgconfig
Interface Python with pkg-config
Papers that mentioned: 3
pypi: tm
Topic Maps
Papers that mentioned: 94
pypi: wordcloud
A little word cloud generator
Papers that mentioned: 39