CLIP-Explorer – Web Server for CLIP-Seq data analysis

CLIP-Explorer

:: DESCRIPTION

Galaxy CLIP-Explorer is a webserver to process, analyse and visualise CLIP-Seq data.

::DEVELOPER

the Freiburg Galaxy Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Heyl F, Maticzka D, Uhl M, Backofen R.
Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis.
Gigascience. 2020 Nov 11;9(11):giaa108. doi: 10.1093/gigascience/giaa108. PMID: 33179042; PMCID: PMC7657819.

Peakhood v0.3 – Individual Site Context Extraction for CLIP-Seq Peak Regions

Peakhood v0.3

:: DESCRIPTION

Peakhood is a tool that takes a set of CLIP-seq peak regions, and for each region individually extracts the most likely site context (transcript or genomic).

::DEVELOPER

Bioinformatics Group Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Conda

:: DOWNLOAD

Peakhood

:: MORE INFORMATION

Citation

Uhl M, Rabsch D, Eggenhofer F, Backofen R.
Peakhood: individual site context extraction for CLIP-seq peak regions.
Bioinformatics. 2021 Nov 4:btab755. doi: 10.1093/bioinformatics/btab755. Epub ahead of print. PMID: 34734974.

CLIPSeqTools 0.1.10 – Suite to analyse CLIP-Seq datasets

CLIPSeqTools 0.1.10

:: DESCRIPTION

CLIPSeqTools is a collection of command line applications used for the analysis of CLIP-Seq datasets. CLIP-Seq stands for UV cross-linking and immunoprecipitation coupled with high-throughput sequencing.

::DEVELOPER

Z. MOURELATOS LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CLIPSeqTools

:: MORE INFORMATION

Citation

Maragkakis M, Alexiou P, Nakaya T, Mourelatos Z.
CLIPSeqTools–a novel bioinformatics CLIP-seq analysis suite.
RNA. 2016 Jan;22(1):1-9. doi: 10.1261/rna.052167.115. Epub 2015 Nov 17. PMID: 26577377; PMCID: PMC4691824.

PIPE-CLIP 1.2.0 alpha – Comprehensive online tool for CLIP-seq Data Analysis

PIPE-CLIP 1.2.0 alpha

:: DESCRIPTION

PIPE-CLIP is a Galaxy framework-based comprehensive online pipeline for reliable analysis of data generated by three types of CLIP-seq protocol: HITS-CLIP, PAR-CLIP and iCLIP.

::DEVELOPER

The Quantitative Biomedical Research Center (QBRC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

 PIPE-CLIP

:: MORE INFORMATION

Citation

Genome Biol. 2014 Jan 22;15(1):R18. doi: 10.1186/gb-2014-15-1-r18.
PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis.
Chen B, Yun J, Kim MS, Mendell JT, Xie Y.

dCLIP 1.7.3 – Comparative CLIP-seq Analyses

dCLIP 1.7.3

:: DESCRIPTION

dCLIP is written in Perl for discovering differential binding regions in two CLIP-Seq (HITS-CLIP or PAR-CLIP) experiments. It is appropiate in experiments where the common binding regions that are significantly enriched in both conditions tend to have similar binding strength and when researchers are more interested in the difference in binding strength rather than the binary event of whether binding site is common or not.

::DEVELOPER

The Quantitative Biomedical Research Center 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 dCLIP

:: MORE INFORMATION

Citation

Genome Biol. 2014 Jan 7;15(1):R11. doi: 10.1186/gb-2014-15-1-r11.
dCLIP: a computational approach for comparative CLIP-seq analyses.
Wang T, Xie Y, Xiao G.

Zagros 1.1.0 – Motif discovery using CLIP-Seq data

Zagros 1.1.0

:: DESCRIPTION

Zagros is a motif discovery software for CLIP-Seq high-throughput protein-RNA interaction data. Given the regions of significant enrichment for reads Zagros can characterize the binding site for the given RBP. Zagros contains two additional programs to calculate the base pairing probabilities of the input sequences and extracting experiment specific events to incorporate such information for an extremely accurate motif discovery.

::DEVELOPER

The Smith Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Zagros

:: MORE INFORMATION

Citation

Leveraging cross-link modification events in CLIP-seq for motif discovery.
Bahrami-Samani E, Penalva LO, Smith AD, Uren PJ.
Nucleic Acids Res. 2015 Jan;43(1):95-103. doi: 10.1093/nar/gku1288.