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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Aristotelis Tsirigos

Publication for GenomicTools

GenomicTools citations

 (6)
library_books

Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD finger protein Phf5a

2016
Nat Cell Biol
PMCID: 5083132
PMID: 27749823
DOI: 10.1038/ncb3424

[…] e 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 3.2.0 […]

call_split

The ubiquitin ligase HUWE1 regulates hematopoietic stem cell maintenance and lymphoid commitment

2016
Nat Immunol
PMCID: 5117833
PMID: 27668798
DOI: 10.1038/ni.3559
call_split See protocol

[…] 1 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 Ge […]

call_split

Genome wide co localization of active EGFR and downstream ERK pathway kinases mirrors mitogen inducible RNA polymerase 2 genomic occupancy

2016
Nucleic Acids Res
PMCID: 5137434
PMID: 27587583
DOI: 10.1093/nar/gkw763
call_split See protocol

[…] stance 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 for TS […]

library_books

Chromatin state analysis of the barley epigenome reveals a higher‐order structure defined by H3K27me1 and H3K27me3 abundance

2015
Plant J
PMCID: 4973852
PMID: 26255869
DOI: 10.1111/tpj.12963

[…] genes 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 to be attrib […]

library_books

FBXW7 modulates cellular stress response and metastatic potential via HSF1 post translational modification

2015
Nat Cell Biol
PMCID: 4401662
PMID: 25720964
DOI: 10.1038/ncb3121

[…] analyses. 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. […]

library_books

Contrasting roles for histone 3 lysine 27 demethylases in acute lymphoblastic leukemia

2014
Nature
PMCID: 4209203
PMID: 25132549
DOI: 10.1038/nature13605

[…] RNA-sequencing data analysis was performed using the DEGseq. MACS version 2.0.10 was used for JMJD3 ChIP-sequencing peak discovery in conjunction with the Irreproducible Discovery Rate (IDR) method.. GenomicTools version 2.7.2 was used for performing genomic interval mathematical operations, genomic interval annotation, H3K27me3 ChIP-sequencing comparisons (GSKJ4 versus control) and ChIP-sequencin […]

Citations

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

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