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chevron_left Topology enrichment analysis Bioinformatics workflows Peak calling Motif comparison Peak clustering chevron_right
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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

Versioning


No version available

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 citations

 (21)
library_books

Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy

2018
BMC Genomics
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 […]

library_books

AICDA drives epigenetic heterogeneity and accelerates germinal center derived lymphomagenesis

2018
Nat Commun
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 […]

library_books

High intensity UV laser ChIP seq for the study of protein DNA interactions in living cells

2017
Nat Commun
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 […]

library_books

Genome wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus

2017
BMC Genomics
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 […]

library_books

Regulation of the BMP Signaling Responsive Transcriptional Network in the Drosophila Embryo

2016
PLoS Genet
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 […]

library_books

The transcriptional repressor Hes1 attenuates inflammation via regulating transcriptional elongation

2016
Nat Immunol
PMCID: 4955730
PMID: 27322654
DOI: 10.1038/ni.3486

[…] than 60 million nonclonal mapped tags were obtained for each condition in each experiment for analysis. the wig files displayed in ucsc genome browser were generated using the bioinformatic program chipseeqer., to identify genes with differential pol ii occupancy on gene body regions, the read counts from the pol ii chip-seq data in specialized genome region were compared. a custom r script […]


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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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