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bamsignals specifications


Unique identifier OMICS_15778
Name bamsignals
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.12.1
Stability Stable
methods, BiocGenerics, IRanges, GenomicRanges, Rsamtools, BiocStyle, zlibbioc, rmarkdown, knitr, Rcpp(>=0.10.6), R(>=3.2.0), testthat(>=0.9)
Maintained Yes




No version available



  • person_outline Alessandro Mammana

bamsignals citations


reChIP seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T cells

Nat Commun
PMCID: 4992058
PMID: 27530917
DOI: 10.1038/ncomms12514

[…] in a window spanning ±750 base pairs from these tsss for input, h3k4me1, h3k4me3, h3k9me3, h3k27ac, h3k27me3, h3k36me3, h3k4me3 rechip and h3k27me3 rechip in r (ref. ) using the bioconductor package bamsignals (version 1.4 for cpg islands, we downloaded the cpg island annotation from ucsc and counted reads along the complete length of the cpg […]


PHF13 is a molecular reader and transcriptional co regulator of H3K4me2/3

PMCID: 4915813
PMID: 27223324
DOI: 10.7554/eLife.10607.094

[…] with the --sjdbgtffile option set to “mus_musculus.grcm38.83.gtf”., differential gene expression was determined by deseq2 (pmid: 25516281). counting was performed using the bioconductor package bamsignals., the chip-seq reads (; ; ; ; ) for each experiment were individually mapped against the mouse genome (genome version mm10) using bowtie2 with default parameters (). the resulting sam file […]

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