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/s12864-017-4353-7

https://doi.org/10.1186/s12864-017-4353-7

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism

Cited by: 72
Author(s): Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J. Taft, Hans R. Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand, Marcos J. Araúzo-Bravo
Published: almost 7 years ago

Software Mentions 21

bioconductor: Biobase
Biobase: Base functions for Bioconductor
Papers that mentioned: 104
bioconductor: bioDist
Different distance measures
Papers that mentioned: 15
bioconductor: GEOquery
Get data from NCBI Gene Expression Omnibus (GEO)
Papers that mentioned: 328
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
cran: directlabels
Direct Labels for Multicolor Plots
Papers that mentioned: 2
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
cran: gplots
Various R Programming Tools for Plotting Data
Papers that mentioned: 2,122
cran: Hmisc
Harrell Miscellaneous
Papers that mentioned: 1,000
cran: pheatmap
Pretty Heatmaps
Papers that mentioned: 2,572
cran: plyr
Tools for Splitting, Applying and Combining Data
Papers that mentioned: 468
cran: raster
Geographic Data Analysis and Modeling
Papers that mentioned: 561
cran: reshape
Flexibly Reshape Data
Papers that mentioned: 123
cran: rpart
Recursive Partitioning and Regression Trees
Papers that mentioned: 431
cran: zoo
S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)
Papers that mentioned: 45
pypi: MACS
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,233
pypi: MACS2
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,203
pypi: MAnorm
A robust model for quantitative comparison of ChIP-Seq data sets
Papers that mentioned: 42
pypi: multicore
Simpler Python multiprocess coding. Persistent workers, memory maps for minimum overhead.
Papers that mentioned: 2
pypi: plyr
UNKNOWN
Papers that mentioned: 468
pypi: reshape
The missing reshape for Python
Papers that mentioned: 123
pypi: zoo
Zoo is a rpc framework for Python
Papers that mentioned: 45