ChIPseeqer protocols

View ChIPseeqer computational protocol

ChIPseeqer statistics

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ChIPseeqer specifications

Information


Unique identifier OMICS_00422
Name ChIPseeqer
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Olivier Elemento <>

Additional information


http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_GUI http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_Tutorial

Publication for ChIPseeqer

ChIPseeqer in pipelines

 (3)
2018
PMCID: 5801776
PMID: 29409445
DOI: 10.1186/s12864-018-4509-0

[…] using bwa-mem aligner v.0.7.15 [], and duplicates were marked and removed using picard-tools v1.107 (http://broadinstitute.github.io/picard). peak detection was performed for each sample by the chipseeqer software [] using the following parameters: length of reads length equal to 101 bp, and length of the fragments equal to 250 bp. the chipseeqer software constructs a read density map […]

2015
PMCID: 4466019
PMID: 26066343
DOI: 10.1371/journal.pone.0129350

[…] fastq files from basecalls and elandv2 aligner was used to align the sequenced reads to the human genome hg19 build using default alignment parameters., peak identification was performed using chipseeqer [] with the read length set to 50bp and default values for all other parameters (for example, peak significance value threshold 10−15 and chip peaks need to be at least 2 fold higher […]

2013
PMCID: 3732535
PMID: 23812588
DOI: 10.1038/nature12287

[…] chip-seq libraries were constructed following the illumina protocol and sequenced on the illumina genome analyzer ii. peak-calling/annotation and consensus sequence analyses were performed with chipseeqer, cisfinder and cisgenome., the shrna against aml1-eto was designed to target the fusion site. other lentiviral shrna sets were purchased from open biosystems. virus preparation and cell […]


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ChIPseeqer in publications

 (20)
PMCID: 5801776
PMID: 29409445
DOI: 10.1186/s12864-018-4509-0

[…] using bwa-mem aligner v.0.7.15 [], and duplicates were marked and removed using picard-tools v1.107 (http://broadinstitute.github.io/picard). peak detection was performed for each sample by the chipseeqer software [] using the following parameters: length of reads length equal to 101 bp, and length of the fragments equal to 250 bp. the chipseeqer software constructs a read density map […]

PMCID: 5768781
PMID: 29335468
DOI: 10.1038/s41467-017-02595-w

[…] all errbs-represented cpgs within the gene body (interval from +2 kb of tss to transcription end site (tes)). genomic distribution of cpgs was determined using the chipseeqerannotate module in the chipseeqer package. significance of genomic distributions of aicda-perturbed cpgs was assessed using a fisher’s exact test vs. all represented, non-perturbed cpgs. to assess a correlation of gene […]

PMCID: 5670203
PMID: 29101361
DOI: 10.1038/s41467-017-01251-7

[…] the corresponding peak summit (x axis, base position of maximum enrichment, ±250 bp) was calculated and plotted over all peaks. conservation analysis was performed using the chipseeqercons module of chipseeqer. conservation scores centered at the peak summit were computed as the mean placental mammal conservation level (phastcons) extracted from hg19 phastcons46way.placental track (ucsc genome […]

PMCID: 5481934
PMID: 28645321
DOI: 10.1186/s12864-017-3866-4

[…] bases using trimmomatic (38) and subsequently mapped to the goat reference genome (chir_1.0 genbank assembly accession: gca_000317765.1, ftp://ftp.ncbi.nih.gov/genomes/capra_hircus) with bwa-sw []., chipseeqer [], a computational framework for the identification of high methylated regions, identified as peaks, across the genome, was used for genome-wide detection of methylation peaks according […]

PMCID: 4933369
PMID: 27379389
DOI: 10.1371/journal.pgen.1006164

[…] parameters were used except from the ‘postprocess’ step that used the flag ‘-a 3’ that allows for unique best matches to be retained along with uniquely mapping reads. peaks were identified using chipseeqer (v2) []; default parameters were used except the fragment length was set to 250bp, and the p-value cut off was set to 4 (the equivalent of 0.0001). the reads shown in the figures […]


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ChIPseeqer institution(s)
HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA; Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
ChIPseeqer funding source(s)
Supported by the CAREER grant from National Science Foundation (DB1054964), as well as by startup funds from the Institute for Computational Biomedicine, Weill Cornell Medical College.

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