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Protocols

seqMINER specifications

Information


Unique identifier OMICS_00460
Name seqMINER
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Laszlo Tora

Publication for seqMINER

seqMINER citations

 (98)
library_books

Mtf2 PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis

2018
PMCID: 5928144
PMID: 29736258
DOI: 10.1038/s41421-018-0022-5

[…] or functional annotation with a Benjamini–Hochberg false discovery rate correction test, unless otherwise indicated,. Repeated k-means clustering analysis of methylation occupancy was completed using seqMINER. ChIP-seq data are available in GEO (GSE72288). […]

call_split

Luminal breast cancer specific circular RNAs uncovered by a novel tool for data analysis

2018
Oncotarget
PMCID: 5865691
PMID: 29581865
DOI: 10.18632/oncotarget.24522
call_split See protocol

[…] omic signal profile around 5ʹ or 3ʹ BS sites. Specifically, ChIP-Seq reads were aligned against hg19 human genome using Bowtie2 in default settings. The genomic signal profile was then computed using seqMINER algorithm v1.3 [] considering a genomic region of +/− 1 kbp centered on the BS sites. The genomic signal normalization was then normalized using NormChIP algorithm []. The number of H3K36me3 […]

library_books

SOX2 regulates common and specific stem cell features in the CNS and endoderm derived organs

2018
PLoS Genet
PMCID: 5825159
PMID: 29432416
DOI: 10.1371/journal.pgen.1007224

[…] . ChIP-seq data was visualized as either track alignments, averaged over 75bp, to genomic positions using IGV v.2.3.88 [,] or as heat maps of raw reads to bed peak files (±5kb from peak center) using Seqminer v.1.2 []. […]

library_books

Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer

2018
Nat Commun
PMCID: 5797120
PMID: 29396493
DOI: 10.1038/s41467-018-02856-2

[…] ng MACS (v1.4) and DFilter (v1.5), where only peaks were considered that were shared by the two peak callers. Genome browser snapshots were generated using IGV (v2.3.67), heatmaps were compiled using SeqMiner (v1.3.3) and genomic region enrichment analysis was performed with CEAS (v1.0.2). To generate consensus peaksets for each factor we used DiffBind (v1.14) with a cutoff defined where a peak mu […]

library_books

Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate

2017
Nat Commun
PMCID: 5727188
PMID: 29233992
DOI: 10.1038/s41467-017-02145-4

[…] nRNA-seq data were subjected to read density analysis after normalisation of all samples per experiment (see above). For heatmaps and average density profiling and differential enrichment profiling, SeqMINER 1.3.3 or DeepTools (http://deeptools.ie-freiburg.mpg.de/) were used to extract read densities at genomic regions (metagenes or TT loci) of interest as indicated in the figures. Heatmaps were […]

library_books

The histone code reader Spin1 controls skeletal muscle development

2017
PMCID: 5775400
PMID: 29168801
DOI: 10.1038/cddis.2017.468

[…] analyzed using a previously deposited GEO data set (GSE36024). Venn diagrams were generated with the help of Venny. Intensity profiles for Spin1 and H3K4me3 gene promoter occupancy were analyzed with SeqMINER. […]

Citations

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seqMINER institution(s)
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 596, Université de Strasbourg, ILLKIRCH, CHU de Strasbourg, France

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