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Protocols

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

Download


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Versioning


No version available

Documentation


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 citations

 (9)
call_split

Different chromatin and DNA sequence characteristics define glucocorticoid receptor binding sites that are blocked or not blocked by coregulator Hic 5

2018
PLoS One
PMCID: 5940187
PMID: 29738565
DOI: 10.1371/journal.pone.0196965
call_split See protocol

[…] reads 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. […]

call_split

Endothelial deletion of Ino80 disrupts coronary angiogenesis and causes congenital heart disease

2018
Nat Commun
PMCID: 5785521
PMID: 29371594
DOI: 10.1038/s41467-017-02796-3
call_split See protocol

[…] n 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 on an initial […]

library_books

CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo

2018
eLife
PMCID: 5826290
PMID: 29481322
DOI: 10.7554/eLife.32341.029

[…] g. ). Results 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. […]

library_books

Derivation of hypermethylated pluripotent embryonic stem cells with high potency

2017
Cell Res
PMCID: 5752839
PMID: 29076502
DOI: 10.1038/cr.2017.134

[…] pe 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. […]

library_books

YEATS2 links histone acetylation to tumorigenesis of non small cell lung cancer

2017
Nat Commun
PMCID: 5651844
PMID: 29057918
DOI: 10.1038/s41467-017-01173-4

[…] reads. 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). […]

library_books

Super enhancers define a proliferative PGC 1α expressing melanoma subgroup sensitive to BET inhibition

2017
Oncogene
PMCID: 5799712
PMID: 28991225
DOI: 10.1038/onc.2017.325

[…] ount of 0.00001 was added to avoid log10(0) during logLR calculation. ChIP-seq tracks were generated using the Integrative Genomics Viewer software., Heatmaps and line plots were generated using the seqplots software (http://przemol.github.io/seqplots). The ChIP-seq data were deposited under GSE95585.The rank ordering of super-enhancers (ROSE) script, was used to generate stitched enhancers and […]

Citations

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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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