SeqPlots protocols

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SeqPlots specifications

Information


Unique identifier OMICS_14234
Name SeqPlots
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Javascript, R
License GNU General Public License version 3.0
Computer skills Medium
Version 1.19.3
Stability Stable
Requirements
mode, seqplots, foundation
Source code URL https://codeload.github.com/Przemol/seqplots/zip/v1.10.6
Maintained Yes

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Maintainer


  • person_outline Przemyslaw Stempor <>

Publication for SeqPlots

library_books

SeqPlots - Interactive software for exploratory data analyses, pattern discovery and visualization in genomics.

2016 Wellcome Open Res
PMCID: 5133382
PMID: 27918597
DOI: 10.12688/wellcomeopenres.10004.1

SeqPlots in pipelines

 (2)
2018
PMCID: 5940187
PMID: 29738565
DOI: 10.1371/journal.pone.0196965

[…] aligned to mitochondrial dna were removed. accessible regions and peaks were identified using the broad peak calling parameters of macs2. chromatin accessibility profiles were created using the seqplots package [] from bioconductor by assessing the chromatin with atac-seq reads per million (rpm) per 10 nucleotides +/- 1kb from the gbr summit., previously we showed that chd9 and brm […]

2017
PMCID: 5554785
PMID: 28787591
DOI: 10.1016/j.devcel.2017.07.002

[…] after normalisation by the library size factor s = c/g (with c: number of covered bases, and g: the size of the genome). images for histone h3k9me3 enrichment on the pirna sensor were prepared with seqplots ()., the mjis588 allele was generated by removing the introns two and three from the gfp sequence in the plasmid pem975 that is used to generate the mjis144 allele. new plasmid is inserted […]


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SeqPlots in publications

 (11)
PMCID: 5940187
PMID: 29738565
DOI: 10.1371/journal.pone.0196965

[…] aligned to mitochondrial dna were removed. accessible regions and peaks were identified using the broad peak calling parameters of macs2. chromatin accessibility profiles were created using the seqplots package [] from bioconductor by assessing the chromatin with atac-seq reads per million (rpm) per 10 nucleotides +/- 1kb from the gbr summit., previously we showed that chd9 and brm […]

PMCID: 5785521
PMID: 29371594
DOI: 10.1038/s41467-017-02796-3

[…] format, replicate-merged, and input into macs2.0 for fold change and p-value signal tracks, . resulting bigwig files were used for all data visualization; heatmaps and profiles were generated using seqplots. in order to rank genes by ino80 occupancy for gsea analysis, promoters were first defined as the window from 1500 bp upstream of the tss to 2000 bp downstream of the tss, based […]

PMCID: 5826290
PMID: 29481322
DOI: 10.7554/eLife.32341.029

[…] were considered significant at *p<0.05, **p<0.01. principal component analyses and correlation matrix plots were produced using deeptools (). average tss signal profiles were made using seqplots r/bioconductor package (). all other figures were produced using the ggplot2 package in r., this paper was supported by the following grant:, http://dx.doi.org/10.13039/100004440wellcome […]

PMCID: 5752839
PMID: 29076502
DOI: 10.1038/cr.2017.134

[…] package., uhc of 2 kb tile methylation was performed using the r hclust command with the “ward” method. correlation matrix was calculated by the r corrplot package. profile plot was created by the r seqplots package. gene ontology analysis was performed by great and david bioinformatics resource 6.8., all the sequencing data were deposited in the ncbi, gene expression omnibus (geo) […]

PMCID: 5651844
PMID: 29057918
DOI: 10.1038/s41467-017-01173-4

[…] clonal reads were automatically removed by macs. the chip-seq profiles were normalized to 10,000,000 total tag numbers, and peaks were called at p ≤ 1e−8. the chip-seq heatmap was drawn by the seqplots r package (http://github.com/przemol/seqplots)., all animal studies were in compliance with ethical regulations at the university of texas md anderson cancer center. female athymic nude mice […]


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SeqPlots institution(s)
The Gurdon Institute and the Department of genetics, University of Cambridge, Cambridge, UK
SeqPlots funding source(s)
This work was supported by the Wellcome Trust (101863).

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