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/s12864-015-2140-x

https://doi.org/10.1186/s12864-015-2140-x

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

Cited by: 54
Author(s): Nathan Harmston, Elizabeth Ing-Simmons, Malcolm Perry, Anja Barešić, Boris Lenhard
Published: about 9 years ago

Software Mentions 15

bioconductor: GenomicInteractions
Utilities for handling genomic interaction data
Papers that mentioned: 10
bioconductor: GenomicRanges
Representation and manipulation of genomic intervals
Papers that mentioned: 323
bioconductor: GOTHiC
Binomial test for Hi-C data analysis
Papers that mentioned: 17
bioconductor: Gviz
Plotting data and annotation information along genomic coordinates
Papers that mentioned: 134
bioconductor: HiTC
High Throughput Chromosome Conformation Capture analysis
Papers that mentioned: 21
bioconductor: r3Cseq
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
Papers that mentioned: 7
bioconductor: Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Papers that mentioned: 138
bioconductor: rtracklayer
R interface to genome annotation files and the UCSC genome browser
Papers that mentioned: 107
cran: data.table
Extension of 'data.frame'
Papers that mentioned: 33
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
cran: gridExtra
Miscellaneous Functions for "Grid" Graphics
Papers that mentioned: 298
cran: igraph
Network Analysis and Visualization
Papers that mentioned: 1,555
cran: stringr
Simple, Consistent Wrappers for Common String Operations
Papers that mentioned: 172
pypi: bowtie
Interactive Dashboard Toolkit.
Papers that mentioned: 1,566
pypi: igraph
High performance graph data structures and algorithms
Papers that mentioned: 1,555