Pyicoclip statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Pyicoclip

Tool usage distribution map

This map represents all the scientific publications referring to Pyicoclip per scientific context
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Pyicoclip specifications


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


No version available



Pyicoclip citations


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

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 […]


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

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, […]


RNA regulatory networks diversified through curvature of the PUF protein scaffold

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–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 […]


Revealing protein–lncRNA interaction

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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