seqMINER protocols

View seqMINER computational protocol

seqMINER statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Read alignment Normalization Tag density plot visualization Peak annotation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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


Add your version

Maintainer


  • person_outline Laszlo Tora <>

Publication for seqMINER

seqMINER in pipelines

 (14)
2018
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 []., toppcluster [] was used to create a network generator fruchterman-reingold output in order to visualize the top 10 go biological process terms with between 1 and 1500 genes, […]

2017
PMCID: 5366954
PMID: 28345651
DOI: 10.1038/srep45365

[…] analysis using ggplot2 in r package (). heat map plots for the indicated histone modifications were determined as counts per million in 25 bp bins in the 10 kb region surrounding the tss using seqminer. peak calling from the chip-seq data was performed using a homer package with default parameters and chromatin input sample as a control. average profile plots and box plots were generated […]

2017
PMCID: 5501531
PMID: 28683804
DOI: 10.1186/s13059-017-1261-8

[…] stimulus, signaling cascades and responses to hormone stimuli, both in control conditions and after flg22 treatment (additional file : figure s24f)., we next compared the two chip-seq datasets using seqminer and diffreps, which allows qualitative and quantitative comparisons to be made between a reference set of genomic positions and multiple chip-seq datasets []. using this approach, […]

2017
PMCID: 5613355
PMID: 28946896
DOI: 10.1186/s13072-017-0153-1

[…] software (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)., the distribution of genes per chromosome, peaks and overlap with chromatin segments was determined with epiexplorer [], and seqminer was used for k-means clustering and heatmap generation []. the spearman correlation of raw data in 10-kb bins and the metagene profiles were generated in deeptools []. the go analysis […]

2016
PMCID: 5007689
PMID: 27588042
DOI: 10.1186/s13072-016-0084-2

[…] data, the illumina reads (50 bp) were aligned to human repeat subgenome generated by trf [] using blat [] (allowing 95 % identity) and/or bowtie [] (with parameters -v 2 --best --strata --tryhard). seqminer [] was used to analyze and plot cage expression data from published datasets. motif elicitation (meme) software [] was used to derive consensus sequences from genomic repeats with parameters […]


To access a full list of citations, you will need to upgrade to our premium service.

seqMINER in publications

 (72)
PMCID: 5928144
PMID: 29736258
DOI: 10.1038/s41421-018-0022-5

[…] 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)., the ezh2 and ring1b chip was performed using clone d2c9 (cell signaling technologies) and clone ab3832 (abcam) respectively. the chip-seq […]

PMCID: 5865691
PMID: 29581865
DOI: 10.18632/oncotarget.24522

[…] 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 […]

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 []., toppcluster [] was used to create a network generator fruchterman-reingold output in order to visualize the top 10 go biological process terms with between 1 and 1500 genes, […]

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

[…] 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 […]

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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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

seqMINER reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review seqMINER