Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Quality control software tools | ChIP sequencing data analysis

The absence of a quality control (QC) system is a major weakness for the comparative analysis of genome-wide profiles generated by next-generation sequencing (NGS). This concerns particularly genome binding/occupancy profiling assays like chromatin…
G T A T C G C T A
phantompeakqual…
Desktop

phantompeakqualtools

Computes quick but highly informative enrichment and quality measures for…

Computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment…

G T A T C G C T A
gcapc
Desktop

gcapc GC Aware Peak Caller

Accounts for GC-content bias separately for effects related to protein binding…

Accounts for GC-content bias separately for effects related to protein binding and differential non-specific binding. gcapc is based on a mixture model. It reduces false-positive peaks for any…

G T A T C G C T A
ChiLin
Desktop

ChiLin

Automates quality controls and data analyses on ChIP-seq and DNase-seq data.…

Automates quality controls and data analyses on ChIP-seq and DNase-seq data. ChiLin generates comprehensive quality control reports that include comparisons with historical data derived from over…

G T A T C G C T A
Zerone
Desktop

Zerone

A ChIP-seq discretizer with built-in quality control. Zerone is powered by a…

A ChIP-seq discretizer with built-in quality control. Zerone is powered by a hidden Markov model with zero-inflated negative multinomial emissions, which allows it to merge several replicates into a…

G T A T C G C T A
SSP
Desktop

SSP Strand-Shift Profile

Provides a more sensitive signal-to-noise ratio (S/N) indicator than current…

Provides a more sensitive signal-to-noise ratio (S/N) indicator than current methods both for point- and broad-source marks and is robust for various cell types and sequencing depth. SSP is a peak…

G T A T C G C T A
CHANCE
Desktop

CHANCE

A standalone package for ChIP-seq quality control and protocol optimization.

A standalone package for ChIP-seq quality control and protocol optimization.

G T A T C G C T A
Coda
Desktop

Coda

Uses convolutional neural networks to learn a mapping from suboptimal to…

Uses convolutional neural networks to learn a mapping from suboptimal to high-quality histone ChIP-seq data. Coda uses a high-dimensional discriminative model to encode a generative noise process.…

G T A T C G C T A
cnvCSEM
Desktop

cnvCSEM CNV-guided ChIP-Seq by expectation-maximization algorithm

Guides multi-read allocation by copy-number variations (CNVs). cnvCSEM is a…

Guides multi-read allocation by copy-number variations (CNVs). cnvCSEM is a flexible framework that takes advantage of the state-of-the-art multi-read allocation algorithms and incorporates CNV…

G T A T C G C T A
BIDCHIPS
Desktop

BIDCHIPS BIas Decomposition of CHIP-seq Signals

A framework to quantify the roles of different types of biases in influencing…

A framework to quantify the roles of different types of biases in influencing the genome-wide ChIP-seq signal using a large compendium of ENCODE datasets. Our model, along with the accompanying…

G T A T C G C T A
CCAT
Desktop

CCAT Control based ChIP-Seq Analysis Tools

A software package for the analysis of ChIP-seq data with negative control.

A software package for the analysis of ChIP-seq data with negative control.

G T A T C G C T A
ABS filter
Desktop

ABS filter

Identification and removal of low-complexity sites in allele-specific analysis…

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.