OpenChrom statistics

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Citations per year

Number of citations per year for the bioinformatics software tool OpenChrom
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Tool usage distribution map

This map represents all the scientific publications referring to OpenChrom per scientific context
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Protocols

OpenChrom specifications

Information


Unique identifier OMICS_23784
Name OpenChrom
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License Eclipse Public License version 1.0
Computer skills Medium
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/OpenChrom

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Versioning


No version available

Documentation


Maintainer


  • person_outline Philip Wenig

Additional information


https://wiki.openchrom.net/

Publication for OpenChrom

OpenChrom citations

 (22)
library_books

Bayesian nonparametric discovery of isoforms and individual specific quantification

2018
Nat Commun
PMCID: 5923247
PMID: 29703885
DOI: 10.1038/s41467-018-03402-w

[…] erated from a chromatin state segmentation computational tool sourcing from the Broad Histone UCSC track for nine factors and nine cell types, DNase I/FAIRE/ChIP synthesis annotations from ENCODE and OpenChrom, and LeafCutter clusters (Supplementary Table ). Sample Gm12878HMM was removed from enrichment analysis due to a non-normal null distribution (KS test, p ≤ 0.01), which is required by VSE (S […]

library_books

Molecular adaptations to phosphorus deprivation and comparison with nitrogen deprivation responses in the diatom Phaeodactylum tricornutum

2018
PLoS One
PMCID: 5825098
PMID: 29474408
DOI: 10.1371/journal.pone.0193335

[…] cation was performed using Agilent ChemStation software (Agilent Technologies, Waldbronn, Germany), AMDIS software (version 2.71; National Institute of Standards and Technology, Boulder, CO, USA) and OpenChrom Community Edition Synge (version 0.6.0) (Peter Wenig; http://www.openchrom.net). GC–MS data integration, normalization (total signal) and alignment were performed using the MetAlign software […]

library_books

The role of floridoside in osmoadaptation of coral associated algal endosymbionts to high salinity conditions

2017
Sci Adv
PMCID: 5559212
PMID: 28835914
DOI: 10.1126/sciadv.1602047

[…] erivatized for GC-MS, and analyzed as described above. All samples were prepared and measured in triplicate. GC-MS data were processed (that is, background subtraction, peak picking, and integration; OpenChrom v. 0.901, Lablicate UG) and MS ionization spectra–identified (NIST MS Software 2.0, Agilent Technologies). Statistical testing was conducted on normalized quantities of metabolites (in nanom […]

library_books

Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture

2017
Nucleic Acids Res
PMCID: 5737680
PMID: 28973462
DOI: 10.1093/nar/gkx680

[…] Regulatory elements were quantified from GRO-seq libraries based on DNase I Hypersensitivity narrow peak coordinates from ENCODE (OpenChrom, Duke University, GSE32970). The peaks were extended ±250 bp from the peak center and merged using BEDTools merge to avoid redundancy. Peaks that were located in a 500-kbp window from both p […]

library_books

Overexpression of BdMATE Gene Improves Aluminum Tolerance in Setaria viridis

2017
Front Plant Sci
PMCID: 5462932
PMID: 28642761
DOI: 10.3389/fpls.2017.00865

[…] rature ramp to 310°C, and a final 1 min of heating at 310°C. Mass spectra were recorded at 2 scan s-1 with a scanning range of 50–600 m/z. Both chromatograms and mass spectra were evaluated using the OpenChrom software (). The peaks were identified and quantified in comparison with authentic standards and the NIST 08 Mass Spectral Library. […]

call_split

Modulation of the growth and metabolic response of cyanobacteria by the multifaceted activity of naringenin

2017
PLoS One
PMCID: 5428994
PMID: 28498848
DOI: 10.1371/journal.pone.0177631
call_split See protocol

[…] 50°C. The flow rate of the carrier gas (helium) was set at 1.5 mL min-1. A split flow of 30 mL min-1 and a split ratio of 20:1 was used. The chromatographic data were recorded and processed using the OpenChrom software []. […]


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OpenChrom institution(s)
Department of Wood Science, University of Hamburg, Hamburg, Germany
OpenChrom funding source(s)
Supported by the Department of Wood Science (University of Hamburg, Germany).

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