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Protocols

deepTools specifications

Information


Unique identifier OMICS_08441
Name deepTools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequence data
Input format BAM
Output data BAM, bigWig, bedGraph, BED
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • bamCoverage

Download


galaxy.png
conda.png

Versioning


No version available

Maintainer


  • person_outline Thomas Manke

Additional information


http://deeptools.readthedocs.io/en/latest/

Information


Unique identifier OMICS_08441
Name deepTools
Interface Web user interface
Restrictions to use None
Input data Sequence data
Input format BAM
Output data BAM, bigWig, bedGraph, BED
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • bamCoverage

Maintainer


  • person_outline Thomas Manke

Additional information


http://deeptools.readthedocs.io/en/latest/

Publication for deepTools

deepTools citations

 (181)
library_books

MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

2018
Nat Commun
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] (version 0.7.15). samtools (version 1.4) was used to split the alignments into mouse and drosophila reads. read normalization via the drosophila melanogaster spike-in material was carried out with deeptools (version 2.5.0.1) for each sample. profile plots of histone marks were also generated with deeptools (version 2.5.0.1). for the comparison of h3k79me2 vs. h3k36me3 signal intensities […]

library_books

Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width

2018
Nat Commun
PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y

[…]  0.05 or q-value < 0.05 was considered statistically significant., heatmaps and average profiles showing the h3k4me3 chip-seq signal were generated with the commands plotheatmap and plotprofile in deeptools. other heatmaps and density scatter plots were created using matlab. all bar graphs, pie graphs, and box plots were created using graphpad prism. in all box plots, the boxes extend between t […]

library_books

NOTCH mediated non cell autonomous regulation of chromatin structure during senescence

2018
Nat Commun
PMCID: 5943456
PMID: 29743479
DOI: 10.1038/s41467-018-04283-9

[…] of peaks (+/−2.5 kb) representing novel accessible regions (regions with significantly altered chromatin accessibility in ris or nis relative to growing cells) with k-means clustering using the deeptools package., samples were normalised with the pre-calculated normalisation factors (as described above in ‘generation of normalised coverage files’), and reads from all growing, ris, nis, […]

library_books

Robust Sub nanomolar Library Preparation for High Throughput Next Generation Sequencing

2018
BMC Genomics
PMCID: 5935984
PMID: 29728062
DOI: 10.1186/s12864-018-4677-y

[…] pile-ups in a snapshot of a random genomic region of the three bordetella bronchiseptica rb50 strains between the two protocols. fib. 2b demonstrates genome-wide similarities of read coverages using deeptools between the two protocols.fig. 2, the third study (mrna libraries) demonstrated that the standard illumina protocol (2 nm → 8.3 pm) and the sub-nanomolar protocol (100 pm → 8.3 pm) […]

library_books

mRNA Cap Methyltransferase, RNMT RAM, Promotes RNA Pol II Dependent Transcription

2018
Cell Rep
PMCID: 5946721
PMID: 29719263
DOI: 10.1016/j.celrep.2018.04.004

[…] with 25 μg hela chromatin as in . libraries for sequencing were prepared as in , and sequencing was performed on illumina nextseq. chip reads were aligned with star, correlations were performed with deeptools, and the read distribution profile was plotted with ngs.plot (, , ). data from replicates were pooled for analysis of gene loci. bedgraphs were visualized using the integrated genome […]

library_books

High Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development

2018
Cell Rep
PMCID: 5965702
PMID: 29719267
DOI: 10.1016/j.celrep.2018.03.129

[…] browser using the kent source tools (v.329) (). correlations of chip-seq signals and principal-component analysis across samples and markfs were calculated in non-overlapping 10-kb windows using deeptools2 (v.2.5.0.1) ()., the accession number for the chip-seq signals, peak calls, and chromatin state segmentations reported in this paper is geo: gse97752., all data can be visualized […]


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deepTools institution(s)
Max Planck Institute of Immunobiology and Epigenetics, Stübeweg, Freiburg, Germany
deepTools funding source(s)
German Research Foundation [SFB 992, Project Z01]; German Epigenome Programme DEEP [01KU1216G]

deepTools review

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Gyan Prakash Mishra

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you have NGS datasets?, wanna know how your data looks like? visualize and explore your sequencing data in terms of correlation, heatmap, BedGraph file to visualize in IGV. This is the best tool.