CLIP-seq data analysis bioinformatics software tools

Cross-Linking Immunoprecipitation associated to high-throughput sequencing (CLIP-seq) is a technique used to identify RNA directly bound to RNA-binding proteins across the entire transcriptome in cell or tissue samples. Recent technological and computational advances permit the…

CLIP-seq analysis steps

Most recent bioinformatics tools

MG Workbench
Dataset

MG Workbench Microbial Genome Workbench

Explores bacterial and archaeal genomes. MG Workbench is a database designed to…

Explores bacterial and archaeal genomes. MG Workbench is a database designed to focus on intra-genomic and inter-genomic comparison of genes and proteins.

ePlant
Web

ePlant

Allows exploration of Arabidopsis thaliana through multiple levels. ePlant…

Allows exploration of Arabidopsis thaliana through multiple levels. ePlant permits researchers to extract information from their data. It can identify connections between layers and facilitate…

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LSTrAP
Desktop

LSTrAP Large-Scale Transcriptome Analysis Pipeline

Pre-processes RNA-seq data and maps it to the genome. LSTrAP performs quality…

Pre-processes RNA-seq data and maps it to the genome. LSTrAP performs quality control and produces co-expression networks. It provides functional and comparative genomics data to enable a host of…

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BisPin
Desktop

BisPin

Maps bisulfite-treated short DNA reads to a reference genome. BisPin is an…

Maps bisulfite-treated short DNA reads to a reference genome. BisPin is an application that supports the hairpin construction strategy and rescores ambiguously mapped reads. It provides biologically…

Most popular analytical software

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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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Bowtie
Desktop

Bowtie

A short read aligner that aligns short DNA sequences (reads) to the human…

A short read aligner that aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its…

ZENBU
Web

ZENBU

Enables data exploration through "on-demand" data processing and…

Enables data exploration through "on-demand" data processing and interactive linked-visualizationsthus enabling concurrent views from the same mere primary sequence alignment data which…

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NGS-QC…
Desktop

NGS-QC Generator

A computational-based approach that infers quality indicators from the…

A computational-based approach that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile.

Curators for CLIP-seq analysis

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