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Pyicoclip specifications

Information


Unique identifier OMICS_08898
Name Pyicoclip
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format eland, SAM, BAM, BED formats
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Eduardo Eyras

Pyicoclip citations

 (4)
library_books

Post transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq

2017
Nat Commun
PMCID: 5662751
PMID: 29084942
DOI: 10.1038/s41467-017-01126-x

[…] P19 cells with dCLIP analysis and selecting peaks with a score greater than 7. For bindings sites of endogenously expressed miRNAs, we analyzed Ago2-miRNA peaks in siSfpq-transfected P19 cells using pyicoclip with the same protocol as described in Bottini et al. In Supplementary Data  is shown the recruited Ago2-let-7a or Ago2-miRNA peaks in siSfpq-transfected P19 cells.Spatial correlation of the […]

library_books

FUS affects circular RNA expression in murine embryonic stem cell derived motor neurons

2017
Nat Commun
PMCID: 5379105
PMID: 28358055
DOI: 10.1038/ncomms14741

[…] rom the Pyicoteo suite were used to call CLIP-Seq peaks. First, all reads were extended to a length of 36 nucleotides using the pyicos extend tool. Then, CLIP-Seq peak calling was performed using the pyicoclip tool. Ensembl 77 GTF file was supplied to generate exploratory regions, using the option --region-magic genebody. For each replicate, only peaks with P value <0.0001 were retained. Finally, […]

library_books

RNA regulatory networks diversified through curvature of the PUF protein scaffold

2015
Nat Commun
PMCID: 4570272
PMID: 26364903
DOI: 10.1038/ncomms9213

[…] ame.sam -5 5 -N 1 -p 8). The .sam files were used to create.bam and indexed.bam files using samtools for visualization of the data in Artemis Genome browser. Peaks were defined using Pyicoteo (python pyicoclip filename.sam -f filename.pk–region Sc.bed–stranded). The .bed file required for Pyicoteo was downloaded from the Saccharomyces Genome Database (SGD). Next, the duplicate peaks were removed f […]

library_books

Revealing protein–lncRNA interaction

2015
Brief Bioinform
PMCID: 4719072
PMID: 26041786
DOI: 10.1093/bib/bbv031

[…] in each cluster reduced the number of false hits. A number of sophisticated algorithms have been developed, e.g. PARalyzer [], Piranha [], wavClusteR [], RIPSeeker [], MiClip [], PIPE-CLIP [] and the Pyicoclip module of the Pyicoteo toolkit (previously called Pyicos) []. While different in implementation, all these procedures can be summarized in the same two steps: (i) clusters identification fro […]

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