EaSeq protocols

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EaSeq specifications

Information


Unique identifier OMICS_10848
Name EaSeq
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Input format Bed, Bam, Aln, BedGraph, Wig, Cod, Text
Output format Bed, Aln, Wig, BedGraph, Text, Tiff
Operating system Mac OS, Windows
Computer skills Medium
Version 0.981
Stability Beta
Maintained Yes

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Documentation


Maintainer


  • person_outline mads.lerdrup <>

Additional information


http://dx.doi.org/10.1038/nsmb.3180

EaSeq in pipeline

2017
PMCID: 5499887
PMID: 28541545
DOI: 10.1093/nar/gkx441

[…] tree of krüppel-like factors and clustalw alignment of klf1/klf3 were performed using the program geneious version r7 (). hierarchical clustering and read density plots were generated using easeq (), available from http://easeq.net/. proportional venn diagrams were generated with use of eulerape ()., the new chip-seq and rna-seq data from this publication have been submitted to the gene […]


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EaSeq in publications

 (8)
PMCID: 5797102
PMID: 29396395
DOI: 10.1038/s41467-018-02939-0

[…] aligned with hg19 assembly by using bowtie for illumina. macs2 was used for peak calling. peaks were annotated by peak2gene for their locations relative to adjacent genes. peaks were visualized by easeq [reference: http://www.nature.com/nsmb/journal/v23/n4/full/nsmb.3180.html]., data are presented as mean ± sd or mean ± sem and subjected to two-tailed unpaired t test. a p value of 0.05 […]

PMCID: 5561104
PMID: 28819152
DOI: 10.1038/s41598-017-08754-9

[…] to classify the epigenome of the experimental model system into a discrete number of chromatin states, subsequently superimposed to the tri cistrome, whereas other integrative tools like seqminer or easeq. exploit the simple co-occurrence of chip-derived patterns, more prone to some bias. in conclusion, our strategy merges new and public algorithms into a coherent process leading to cistrome […]

PMCID: 5521770
PMID: 28732065
DOI: 10.1371/journal.pone.0180922

[…] and western blotting, as per encode recommendations []., computational analysis of raw sequencing data was performed as previously described []. heatmaps of signal intensity were generated using easeq [] and regions were sorted according to hierarchical clustering using the nearest neighbour chain algorithm. clustering was based on values from all datasets quantified from 200 bp surrounding […]

PMCID: 5468232
PMID: 28607444
DOI: 10.1038/s41598-017-03534-x

[…] the cancer types. it was observed that the peaks were significantly higher in both the cancer type as compared to peaks in the normal sample (fig. ).figure 3 , the enrichment plots obtained from easeq displayed differences in the overall distribution of expressed regions in fig. . the r value or the correlation coefficient, which indicates the linear relationship between two variables […]

PMCID: 5499887
PMID: 28541545
DOI: 10.1093/nar/gkx441

[…] p300 chip-seq in mel cells (encff001nxl), dnase1-seq in mel cells (encff001oob), and h3k4me3 chip-seq in mel cells (encff001mzr). we compared read densities between chip-seq data sets using easeq ()., cage data () was extracted from the zenbu genome browser () fantom5 mouse time course study (). the phase2 pooled data from the j2e differentiation time course in response to epo […]


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EaSeq institution(s)
Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
EaSeq funding source(s)
Supported by a grant from the Danish National Research Foundation (DNRF82).

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