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/s13072-016-0095-z

https://doi.org/10.1186/s13072-016-0095-z

EpiMINE, a computational program for mining epigenomic data

Cited by: 11
Author(s): Sri Ganesh Jammula, Diego Pasini
Published: about 8 years ago

Software Mentions 23

bioconductor: ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
Papers that mentioned: 145
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: DiffBind
Differential Binding Analysis of ChIP-Seq Peak Data
Papers that mentioned: 217
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
cran: bnlearn
Bayesian Network Structure Learning, Parameter Learning and Inference
Papers that mentioned: 113
cran: caret
Classification and Regression Training
Papers that mentioned: 630
cran: FactoMineR
Multivariate Exploratory Data Analysis and Data Mining
Papers that mentioned: 1,101
cran: fastcluster
Fast Hierarchical Clustering Routines for R and 'Python'
Papers that mentioned: 36
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
cran: igraph
Network Analysis and Visualization
Papers that mentioned: 1,555
cran: kernlab
Kernel-Based Machine Learning Lab
Papers that mentioned: 157
cran: RColorBrewer
ColorBrewer Palettes
Papers that mentioned: 490
cran: ROCR
Visualizing the Performance of Scoring Classifiers
Papers that mentioned: 596
cran: STAR
Spike Train Analysis with R
Papers that mentioned: 5,759
pypi: bnlearn
Python package for learning the graphical structure of Bayesian networks, parameter learning, inference and sampling methods.
Papers that mentioned: 113
pypi: caret
A Python Interface to Asterisk
Papers that mentioned: 630
pypi: fastcluster
Fast hierarchical clustering routines for R and Python.
Papers that mentioned: 36
pypi: igraph
High performance graph data structures and algorithms
Papers that mentioned: 1,555
pypi: MACS
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,233
pypi: pybedtools
Wrapper around BEDTools for bioinformatics work
Papers that mentioned: 48
pypi: pysam
Package for reading, manipulating, and writing genomic data
Papers that mentioned: 130
pypi: rpy2
Python interface to the R language (embedded R)
Papers that mentioned: 40
pypi: TopHat
TopHat Platform
Papers that mentioned: 5,017