GenomicTools protocols

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GenomicTools specifications

Information


Unique identifier OMICS_02144
Name GenomicTools
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.7.1a
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Aristotelis Tsirigos <>

Publication for GenomicTools

GenomicTools in pipelines

 (2)
2016
PMCID: 5083132
PMID: 27749823
DOI: 10.1038/ncb3424

[…] aligned against the mouse genome assembly mm10/grcm38. alignments were performed using bowtie v.1.0.0. macs 1.4.2 or macs 2.0 was used for peak-calling in the case of chip-seq data, while the suite genomictools version 2.8.1 was used for genome binning, genomic annotations and the construction of occupancy profiles, both in the case of polymerases and histone marks. for plotting, r version […]

2016
PMCID: 5117833
PMID: 27668798
DOI: 10.1038/ni.3559

[…] in order to report only unique alignments). macs version 2.0.10 was used to perform peak calling for both broad and narrow peaks. the files with the aligned reads were converted to wig format using genomictools and then to bigwig format using the corresponding ucsc tool (wigtobigwig, ucsc browser binary utilities) in order to visualize the tracks. snapshots were prepared using the integrative […]


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GenomicTools in publications

 (6)
PMCID: 5803259
PMID: 29416042
DOI: 10.1038/s41467-018-03017-1

[…] interacting fragments. mapped read pairs were subsequently filtered for known artifacts of the hi-c protocol, such as self-ligation, mapping too far from the enzyme’s known cutting sites, etc, using genomictools gtools-hic filter command. more specifically, reads mapping in multiple locations on the reference genome (multihit), double-sided reads that mapped to the same enzyme fragment […]

PMCID: 5083132
PMID: 27749823
DOI: 10.1038/ncb3424

[…] aligned against the mouse genome assembly mm10/grcm38. alignments were performed using bowtie v.1.0.0. macs 1.4.2 or macs 2.0 was used for peak-calling in the case of chip-seq data, while the suite genomictools version 2.8.1 was used for genome binning, genomic annotations and the construction of occupancy profiles, both in the case of polymerases and histone marks. for plotting, r version […]

PMCID: 5137434
PMID: 27587583
DOI: 10.1093/nar/gkw763

[…] from tss to tts as 3000 bp length, so that the normalized frame size was 50 bp. in both visualizations, the plot was smoothed using running median algorithm. both profiles were generated using genomictools () and visualization was performed in r., violin plots were generated for normalized gene length and at the nearest peaks defined with bins spanning range of 200–250 and 2900–2950 bp […]

PMCID: 4973852
PMID: 26255869
DOI: 10.1111/tpj.12963

[…] and 7063 mid‐expression genes. the total numbers of low‐expression transcripts were 17 882, 21 852 and 18 105, respectively, for low‐, mid‐ and high‐expression transcripts., the software package genomictools (tsirigos et al., ) was used to relate peaks to gene transcripts using the program genomic overlaps offset. peaks were required to be within 1.5 kb of the tss or tes in order […]

PMCID: 4401662
PMID: 25720964
DOI: 10.1038/ncb3121

[…] bowtie version 0.12.7 was used for alignment of sequenced reads. rna-sequencing data analysis was performed using the degseq. macs version 1.4.2 was used for chip-sequencing peak discovery. genomictools version 2.7.2 was used for performing genomic interval mathematical operations, genomic interval annotations and chip-seq profile construction., hsf1 chip-sequenced reads were aligned […]


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GenomicTools institution(s)
Computational Biology Center, IBM TJ Watson Research Center, Yorktown Heights, NY, USA

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