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/s13072-021-00390-y

https://doi.org/10.1186/s13072-021-00390-y

Molecular and computational approaches to map regulatory elements in 3D chromatin structure

Cited by: 7
Author(s): Beoung Hun Lee, Suhn Kyong Rhie
Published: over 3 years ago

Software Mentions 21

bioconductor: ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
Papers that mentioned: 161
bioconductor: DiffBind
Differential Binding Analysis of ChIP-Seq Peak Data
Papers that mentioned: 217
bioconductor: FitHiC
Confidence estimation for intra-chromosomal contact maps
Papers that mentioned: 6
bioconductor: GOTHiC
Binomial test for Hi-C data analysis
Papers that mentioned: 17
bioconductor: HiTC
High Throughput Chromosome Conformation Capture analysis
Papers that mentioned: 21
bioconductor: methylKit
DNA methylation analysis from high-throughput bisulfite sequencing results
Papers that mentioned: 154
bioconductor: minfi
Analyze Illumina Infinium DNA methylation arrays
Papers that mentioned: 506
bioconductor: multiHiCcompare
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Papers that mentioned: 1
bioconductor: sesame
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
Papers that mentioned: 2
cran: HiCseg
Detection of domains in HiC data
Papers that mentioned: 17
cran: TAG
Transformed Additive Gaussian Processes
Papers that mentioned: 66
cran: TopDom
An Efficient and Deterministic Method for Identifying Topological Domains in Genomes
Papers that mentioned: 31
pypi: arrowhead
micro-framework for flowchart-like computing
Papers that mentioned: 1
pypi: bam
Text snippets on the command line.
Papers that mentioned: 10
pypi: Distiller
Automatic Keyword Extraction from Document Collections
Papers that mentioned: 70
pypi: hichipper
Processing HiChIP data into loops.
Papers that mentioned: 10
pypi: MACE

Papers that mentioned: 72
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: Micro
Celery platform to create microservices
Papers that mentioned: 53
pypi: sesame
Encryption tool for application configs.
Papers that mentioned: 2