PeakRanger statistics

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PeakRanger specifications

Information


Unique identifier OMICS_00451
Name PeakRanger
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MapReduce
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes

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Publication for PeakRanger

PeakRanger in pipelines

 (6)
2017
PMCID: 5496309
PMID: 28676099
DOI: 10.1186/s13072-017-0140-6

[…] data were controlled for general quality features using fastqc. unambiguously mapped and unique reads were kept for subsequent generation of binding profiles and calling of peaks using macs and peakranger [] using reads derived from sequencing of input dna as control. peaks were called at p < 10−5 and fdr <5%. all downstream analyses were done in r/bioconductor […]

2015
PMCID: 4549315
PMID: 26305466
DOI: 10.1371/journal.pntd.0003853

[…] the random sampling step drastically reduces the amount of false positives without lowering the sensitivity. mostly, this removes background peaks. identification of peaks was done with ranger of peakranger v1.16 [] with p value cut off 0.0001, fdr cut off 0.01, read extension length 200, smoothing bandwidth 99 and delta 1. we used the input samples as negative controls for the peakcalling […]

2015
PMCID: 4549315
PMID: 26305466
DOI: 10.1371/journal.pntd.0003853

[…] was also used to correlate transcription and histone modification, and to quantify the proportion of peaks that contribute significantly to the average profiles. common peaks were detected from peakranger region bed-files with multiintersectbed of the bedtools package., for the analysis of chromatin structure around repetitive sequences, reads were aligned to a fasta file containing […]

2014
PMCID: 4371837
PMID: 25250711
DOI: 10.7554/eLife.04235.017

[…] significance threshold was set for both. the data sets were then swapped and analyzed for regions with decreased levels of h3k27me3. to get the reads for histograms shown in , the ‘wig’ module of peakranger parsed all aligned reads and counted reads within the specified regions. to find the rest-binding motif (re1), rest peak coordinates were used as input for fimo (). previously published […]

2013
PMCID: 3878573
PMID: 24120743
DOI: 10.1016/j.stem.2013.09.003

[…] nanograms of dna was amplified and single end sequenced at 36 bp, and reads were mapped to the mouse genome (mm9) using bowtie (). peaks were detected against rabbit igg control using macs () and peakranger (). peaks in different experiments were called as the same bound region if the summits fell within 70 bp. to identify peaks bound in one experiment but not another, we defined “nonbound” […]


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PeakRanger in publications

 (16)
PMCID: 5876398
PMID: 29599503
DOI: 10.1038/s41467-018-03668-0

[…] data in the bam format; [http://broadinstitute.github.io/picard/]) to avoid pcr artifacts leading to multiple copies of the same original fragment (see supplementary table ). the encode peak caller peakranger 1.18 was employed in ccat-mode to accommodate for broad peaks. peakranger automatically normalizes input and treatment reads and calls peaks taking the background distribution […]

PMCID: 5754749
PMID: 29203652
DOI: 10.1073/pnas.1618075114

[…] chip-seq data for quality control, read mapping, normalization, peak-calling, and assessment of reproducibility among biological replicates (). the tools “ranger” and “wig” were used in the software peakranger () to identify read-enriched genomic regions (p = 1 × 10−6, q-value = 0.01, remainder of parameters set to default settings) and to generate variable-step wiggle files of read coverage. […]

PMCID: 5676741
PMID: 29116202
DOI: 10.1038/s41467-017-01393-8

[…] were mapped to the human genome (hg19) using bowtie (version 1.0.1), allowing up to three mismatches. non-uniquely alignable reads were excluded., for h2az and h2azac, broad peaks were called using peakranger (version 1.16), peaks from replicates were combined by taking overlapping regions. peaks for rna pol ii, ar, and other transcription factors were called using macs2 the irreproducibility […]

PMCID: 5537105
PMID: 28794828
DOI: 10.1016/j.csbj.2017.07.002

[…] using big data frameworks in other bioinformatics fields, such as autodockcloud, a tool for drug discovery through virtual molecular docking which utilises the hadoop mapreduce framework and peakranger, a tool for calling peaks from chromatin immunoprecipitation sequencing (chip-seq) data also on the mapreduce framework ., the central methodological concept for dealing with scalability […]

PMCID: 5496309
PMID: 28676099
DOI: 10.1186/s13072-017-0140-6

[…] data were controlled for general quality features using fastqc. unambiguously mapped and unique reads were kept for subsequent generation of binding profiles and calling of peaks using macs and peakranger [] using reads derived from sequencing of input dna as control. peaks were called at p < 10−5 and fdr <5%. all downstream analyses were done in r/bioconductor […]


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PeakRanger institution(s)
Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA; Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, USA; Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Institute for Genomics & Systems Biology, The University of Chicago, Chicago, IL, USA
PeakRanger funding source(s)
This project was funded by the iPlant Collaborative and a grant from the National Science Foundation Plant Cyberinfrastructure Program (#DBI-0735191).

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