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Protocols

RepEnrich specifications

Information


Unique identifier OMICS_09502
Name RepEnrich
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Nicola Neretti

Publication for RepEnrich

RepEnrich citations

 (10)
call_split

Transient reduction of DNA methylation at the onset of meiosis in male mice

2018
PMCID: 5883305
PMID: 29618374
DOI: 10.1186/s13072-018-0186-0
call_split See protocol

[…] ed. A final table containing logFC (is log2FC), logCPM (is log2CPM), p value and FDR value for each gene was obtained.For the analysis of the transcriptional landscape of repetitive elements, we used RepEnrich according to the suggested protocol []. Briefly, we aligned RNA-seq data to the genome using Bowtie 1 parameters that allow only unique mapping (-m1) and outputted multi-mapping and uniquely […]

library_books

Transcriptional landscape of human endogenous retroviruses (HERVs) and other repetitive elements in psoriatic skin

2018
Sci Rep
PMCID: 5847543
PMID: 29531256
DOI: 10.1038/s41598-018-22734-7

[…] describing the genome-wide expression pattern of HERVs and repetitive elements in the context of psoriasis. In the present study, we re-analysed our previously published RNA-seq data,, utilizing the RepEnrich pipeline in order to investigate the genome-wide transcriptional landscape of HERVs and repetitive elements in the lesional and non-lesional skin of psoriasis patients. […]

library_books

ROP: dumpster diving in RNA sequencing to find the source of 1 trillion reads across diverse adult human tissues

2018
Genome Biol
PMCID: 5857127
PMID: 29548336
DOI: 10.1186/s13059-018-1403-7

[…] t with 50% relative abundance (Additional file : Figure S3). Among SVA retrotransposons, SVA-D was the most abundant element with 50% relative abundance (Additional file : Figure S4). Consistent with repEnrich [], when using in-house data, we observe the differences in proportions of L1 and Alu elements between poly(A) and ribo-depletion libraries. Among the repeat reads, poly(A) samples have the […]

call_split

Analysis of the Expression of Repetitive DNA Elements in Osteosarcoma

2017
Front Genet
PMCID: 5714928
PMID: 29250102
DOI: 10.3389/fgene.2017.00193
call_split See protocol

[…] ap multiple locations. The mapping confidence was more than 90 because the quality threshold was set to 10. Reads were filtered out if the score was < 10. Mapping quality was at an average of 30. The RepEnrich pipeline with RepeatMasker hg19 library as reference was used for obtaining read counts based on reads aligning to repeated element loci. […]

library_books

­­­Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia­­

2017
PMCID: 5674883
PMID: 28887438
DOI: 10.1083/jcb.201612160

[…] hg19 with Bowtie 2.2.4 and processed with MACS2 (; ). Peak calling was performed with both broad- and narrow-peak functions using a bandwidth of 150, tag size of 50, and q-value cut-off of 0.05. The RepEnrich pipeline was used to determine H3K9me3 levels over TEs. This pipeline generates fractional counts for each element. Fractional counts are generated by quantifying reads that map exclusively […]

call_split

Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA nucleosome association and RNA:DNA hybrid formation

2017
eLife
PMCID: 5538826
PMID: 28760199
DOI: 10.7554/eLife.25293.023
call_split See protocol

[…] Using the RNA-seq alignment files, coverage over repeat elements (MSR, minor satellites, LINE L1MdA and SINE B1) present in the RepeatMasker mouse mm10 genome annotation was determined using RepEnrich (), with the following modifications. First, in order to process the RNA-seq alignment files for RepEnrich, uniquely and multiply mapping reads were separated from the alignment file using S […]

Citations

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RepEnrich institution(s)
Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA; Division of Applied Mathematics, Brown University, Providence, RI, USA; Center for Computational Molecular Biology, Brown University, Providence, RI, USA

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