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Mango specifications

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Unique identifier OMICS_08783
Name Mango
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTQ
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Requirements
R, bedtools, bowtie, MACS
Maintained Yes

Versioning


No version available

Documentation


Publication for Mango

Mango citations

 (3)
library_books

Transcriptional interference by small transcripts in proximal promoter regions

2018
Nucleic Acids Res
PMCID: 5815073
PMID: 29309647
DOI: 10.1093/nar/gkx1242

[…] .bed and b.bed and -r = fraction of overlap reciprocal for a.bed and b.bed) (). ChIA-PET interaction data was normalized for differential peak enrichment and identification of genomic proximity using Mango with default parameters (). […]

library_books

Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin

2017
Sci Rep
PMCID: 5663946
PMID: 29089515
DOI: 10.1038/s41598-017-14389-7

[…] ool were obtained from,. Accession numbers for these datasets are as follows: MCF-7 (GSE39495), K562 (GSE39495), and GM12878 (GSE72816). ChIA-PET Tool interactions were preferred over the alternative Mango, since calls obtained via Mango were sparse and did not include as many broad domain or super enhancer interactions (TableĀ ). To minimize the number of false positive interactions, we instead fi […]

library_books

Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast

2016
Nat Genet
PMCID: 5042855
PMID: 27548313
DOI: 10.1038/ng.3647

[…] To elucidate how condensin and cohesin build association networks across the genome, we focused on significant associations among association spots. The recently developed algorithm, Mango, predicts association spots and significance of the observed associations by considering the distance-dependent background association frequency,. Note that the association spots predicted by th […]


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Mango institution(s)
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
Mango funding source(s)
NIH grant U54HG006996, R00HG007356; Damon Runyon Cancer Research Foundation (DRG-2122-12)

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