Papers: 10.1371/journal.pone.0016432
https://doi.org/10.1371/journal.pone.0016432
An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq
Cited by: 41
Author(s): Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphaël Gottardo
Published: over 14 years ago
Software Mentions 11
Very Likely Science (65)
bioconductor: BSgenome
Software infrastructure for efficient representation of full genomes and their SNPsPapers that mentioned: 47
Very Likely Science (90)
bioconductor: ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome rangesPapers that mentioned: 145
Very Likely Science (76)
bioconductor: GenomicRanges
Representation and manipulation of genomic intervalsPapers that mentioned: 323
Very Likely Science (90)
bioconductor: IRanges
Foundation of integer range manipulation in BioconductorPapers that mentioned: 62
Very Likely Science (75)
Very Likely Science (90)
Very Likely Science (90)
bioconductor: rtracklayer
R interface to genome annotation files and the UCSC genome browserPapers that mentioned: 107
Very Likely Science (90)
cran: JASPAR
R modules for JASPAR databases: a collection of transcription factor DNA-binding preferences, modeled as matricesPapers that mentioned: 1,283
Very Likely Science (75)
Very Likely Science (75)
pypi: STAMP
A graphical software package for analyzing taxonomic and functional profiles.Papers that mentioned: 1,190
Very Likely Science (65)