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/s12859-016-1125-3

https://doi.org/10.1186/s12859-016-1125-3

Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis

Cited by: 3
Author(s): Nathan James Allen Cormier, Tyler Kolisnik, Mark Bieda
Published: over 8 years ago

Software Mentions 10

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: chipseq
chipseq: A package for analyzing chipseq data
Papers that mentioned: 9
bioconductor: gage
Generally Applicable Gene-set Enrichment for Pathway Analysis
Papers that mentioned: 45
bioconductor: GOstats
Tools for manipulating GO and microarrays
Papers that mentioned: 368
bioconductor: pathview
a tool set for pathway based data integration and visualization
Papers that mentioned: 144
cran: knitr
A General-Purpose Package for Dynamic Report Generation in R
Papers that mentioned: 157
cran: seqminer
Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
Papers that mentioned: 4
pypi: bowtie
Interactive Dashboard Toolkit.
Papers that mentioned: 1,566
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