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Normalization software tools | ChIP sequencing data analysis

Chip-seq experiments are becoming a standard approach for genome-wide profiling protein-DNA interactions, such as detecting transcription factor binding sites, histone modification marks and RNA Polymerase II occupancy. However, when comparing a…
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MAnorm
Desktop

MAnorm

A simple and effective method for quantitative comparison of ChIP-Seq data sets…

A simple and effective method for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences…

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Brundle
Desktop

Brundle

Allows normalization of ChIP-Seq data. Brundle implements functions using…

Allows normalization of ChIP-Seq data. Brundle implements functions using spike-in or a second factor as a control for normalization.

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hppRNA
Desktop

hppRNA

Converts the raw fastq files into gene/isoform expression matrix and…

Converts the raw fastq files into gene/isoform expression matrix and differentially expressed genes or isoforms. hppRNA is a one-in-all solution composed of four scenarios such as pre-mapping,…

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POLYPHEMUS
Desktop

POLYPHEMUS

Integrates read-count signal intensity profiles with RNA Polymerase II binding…

Integrates read-count signal intensity profiles with RNA Polymerase II binding site annotations to identify coding regions associated with potential transcriptional activity. Furthermore, POLYPHEMUS…

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miARma-Seq
Desktop

miARma-Seq

Designed for mRNA, miRNA and circRNA identification and differential expression…

Designed for mRNA, miRNA and circRNA identification and differential expression analysis, applicable to any sequenced organism. miARma-Seq is presented as a stand-alone tool that provides different…

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normR
Desktop

normR normR obeys regime mixture rules

A tool for normalization and difference calling in ChIP-seq data. normR…

A tool for normalization and difference calling in ChIP-seq data. normR performs normalization and difference calling simultaneously to identify genomic regions enriched by the ChIP-procedure. In…

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ChIPCor
Desktop

ChIPCor

A testing procedure for evaluating the significance of overlapping from a pair…

A testing procedure for evaluating the significance of overlapping from a pair of proteins by leveraging information from publicly available data. By borrowing information from protein binding…

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Epimetheus
Desktop

Epimetheus

Enables optimal processing of datasets from different enrichment patterns.…

Enables optimal processing of datasets from different enrichment patterns. Epimetheus is a quantile-based multi-profile normalization tool. Users have the possibility to exclude specific genomic…

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chip_diagnostic…
Desktop

chip_diagnostics

A diagnostic tool to examine the appropriateness of the estimated normalization…

A diagnostic tool to examine the appropriateness of the estimated normalization procedure. By plotting the empirical densities of log relative risks in bins of equal read count, along with the…

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ChIPnorm
Desktop

ChIPnorm

A two-stage statistical method to normalize ChIP-seq data, and to find…

A two-stage statistical method to normalize ChIP-seq data, and to find differential regions in the genome, given two libraries of histone modifications of different cell types. ChIPnorm method…

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NCIS
Desktop

NCIS Normalization of ChIP-seq

A method for estimating the normalization factor between the ChIP and the…

A method for estimating the normalization factor between the ChIP and the control samples. NCIS can accommodate both low and high sequencing depth datasets. It shows excellent statistical properties…

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