dREG 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 Data analysis chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

dREG specifications

Information


Unique identifier OMICS_07951
Name dREG
Alternative name discriminative Regulatory-Element detection from GRO-seq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Database management system MySQL
Computer skills Advanced
Stability Stable
Requirements
R, mysql-dev, bigWig
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Charles Danko <>

Additional information


https://dreg.dnasequence.org/pages/doc

Information


Unique identifier OMICS_07951
Name dREG
Alternative name discriminative Regulatory-Element detection from GRO-seq
Interface Web user interface
Restrictions to use None
Input format BIGWIG
Computer skills Basic
Stability Stable
High performance computing Yes
Registration required Yes
Maintained Yes

Download


Documentation


Maintainer


  • person_outline Charles Danko <>

Additional information


https://dreg.dnasequence.org/pages/doc

Publications for discriminative Regulatory-Element detection from GRO-seq

dREG in pipelines

 (2)
2018
PMCID: 5880349
PMID: 29608602
DOI: 10.1371/journal.pone.0194023

[…] the bigwig software package, available from: https://github.com/andrelmartins/bigwig. all data processing and visualization was done in the r statistical environment[]., we identified tres using dreg []. data collected from all four cell lines (tamr and tams mcf-7 cells) was combined to increase statistical power for the discovery of a superset of tres active during any of the conditions […]

2017
PMCID: 5650465
PMID: 29053721
DOI: 10.1371/journal.pone.0186331

[…] to a reference genome comprised of canfam3.1 and a single copy of the pol i ribosomal rna (genbank u13369.1). samples were visualized using custom track hubs on the washu epigenome browser []. the dreg software program was used to identify the location of promoters and active enhancers in combined pro-seq data [], combining male and female samples to improve statistical power for identifying […]


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

dREG in publications

 (6)
PMCID: 5882141
PMID: 29614078
DOI: 10.1371/journal.pone.0194522

[…] experimental procedures). pro-seq library preparation were executed according to illumina protocol and were sequenced using the illumina nextseq500 sequencing., tres were identified using dreg []. data collected between different time points (gdnf treatment) was combined to increase statistical power for the discovery of tres. we used our dreg-hd [] to locate precise coordinates […]

PMCID: 5880349
PMID: 29608602
DOI: 10.1371/journal.pone.0194023

[…] groups of active enhancers [–], and results in enhancer predictions that are highly similar to the canonical active enhancer mark, acetylation of histone 3 at lysine 27 (h3k27ac) [,,]. we used our dreg software package [] followed by a peak refinement that identifies the regions between divergent paused rna polymerase [] to identify 39,753 tres that were active in either the tams or tamr mcf-7 […]

PMCID: 5650465
PMID: 29053721
DOI: 10.1371/journal.pone.0186331

[…] to a reference genome comprised of canfam3.1 and a single copy of the pol i ribosomal rna (genbank u13369.1). samples were visualized using custom track hubs on the washu epigenome browser []. the dreg software program was used to identify the location of promoters and active enhancers in combined pro-seq data [], combining male and female samples to improve statistical power for identifying […]

PMCID: 5557961
PMID: 28811569
DOI: 10.1038/s41467-017-00151-0

[…] significant due to the activity of adjacent or partially overlapping genes (run-over transcription or internal tss), or due to changed transcription of internal regulatory element(s), we utilized dreg. dreg is a machine-based learning method that identifies transcribed regulatory elements from the human genome using support vector regression. to call a gene significantly changed, unchanged […]

PMCID: 5427898
PMID: 28273906
DOI: 10.1038/s41598-017-00176-x

[…] in c2c12 myoblasts – 4,315 enhancers detected based on epigenomic data which will be referred to as blum enhancers, and 5,570 putative enhancer sites identified using our gro-seq data and the dreg method developed by danko et al. , which will be referred to as dreg enhancers (supplementary table ). the two methods apparently identified two distinct sets of enhancers in that only 182 pairs […]


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

dREG institution(s)
Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA; Graduate field of Computational Biology, Cornell University, Ithaca, NY, USA; Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA

dREG reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review dREG