:: DESCRIPTION
PAR-CLIP is a high-throughput method to identify binding sites of RNA binding proteins.
::DEVELOPER
Institute for Bioinformatics, Ludwig-Maximilians-Universität München
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PARma: identification of microRNA target sites in Argonaute PAR-CLIP data.
Erhard F, Dolken L, Jaskiewicz L, Zimmer R.
Genome Biol. 2013 Jul 29;14(7):R79.
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:: DESCRIPTION
BackCLIP is a tool to identify the presence of common RNA background in a PAR-CLIP dataset.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BackCLIP: a tool to identify common background presence in PAR-CLIP datasets.
Reyes-Herrera PH, Speck-Hernandez CA, Sierra CA, Herrera S.
Bioinformatics. 2015 Jul 29. pii: btv442.
:: DESCRIPTION
PARalyzer is a tool for mapping high-confidence sites from PAR-CLIP (photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation) deep-sequencing data.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2011 Aug 18;12(8):R79. doi: 10.1186/gb-2011-12-8-r79.
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.
Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U.
:: DESCRIPTION
BMix is a toolbox for analysing PAR-CLIP data and detecting T-to-C substitutions induced following RNA-protein cross-linking.
::DEVELOPER
the Computational Biology Group (CBG)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMix: Probabilistic modeling of occurring substitutions in PAR-CLIP data.
Golumbeanu M, Mohammadi P, Beerenwinkel N.
Bioinformatics. 2015 Sep 5. pii: btv520.
:: DESCRIPTION
PAR-CLIP HMM (rcpphmmparclip) provides an integrative model to establish a joint distribution of read and mutation counts. To pinpoint the interaction sites at single base-pair resolution, we adopts non-homogeneous hidden Markov models that incorporate the nucleotide sequence.
::DEVELOPER
The Quantitative Biomedical Research Center
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Biometrics. 2014 Jun;70(2):430-40. doi: 10.1111/biom.12147. Epub 2014 Feb 24.
Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP.
Yun J1, Wang T, Xiao G.
