Tag: ChIP-seq

diffReps 1.55.6 – Finding Differential Chromatin Modification Sites from ChIP-seq data

diffReps 1.55.6

:: DESCRIPTION

diffReps is developed to find different peaks in ChIP-seq. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. diffReps takes into account the biological variations within a group of samples and uses that information to enhance the statistical power. Considering biological variation is of high importance, especiallly for in vivo brain tissues.

::DEVELOPER

SHEN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  diffReps

:: MORE INFORMATION

Citation

PLoS One. 2013 Jun 10;8(6):e65598. doi: 10.1371/journal.pone.0065598. Print 2013.
diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates.
Shen L, Shao NY, Liu X, Maze I, Feng J, Nestler EJ.

hiddenDomains 3.1 – A modern HMM to Identify ChIP-seq Enrichment

hiddenDomains 3.1

:: DESCRIPTION

hiddenDomains uses a Hidden Markov Model to identify enriched domains in ChIP-seq data. It accepts BAM files for input and can perform an analysis with or without control data. The output is a BED file, ready for the UCSC genome browser, that contains the domains and is color coded according to their posterior probabilities.

::DEVELOPER

hiddenDomains team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Perl
  • R

:: DOWNLOAD

 hiddenDomains

:: MORE INFORMATION

Citation

Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains.
Starmer J, Magnuson T.
BMC Bioinformatics. 2016 Mar 24;17(1):144. doi: 10.1186/s12859-016-0991-z.

ChIPComp 1.23.0 – Quantatitive Comparison of multiple ChIP-seq dataset

ChIPComp 1.23.0

:: DESCRIPTION

ChIPComp is an R package for quantatitive comparison of multiple ChIP-seq datasets. ChIPComp improves the differential protein binding or histone modification analyses for ChIP-seq data by properly considering the background information from control samples and different signal to noise ratios. ChIPComp also works for general experimental design.

::DEVELOPER

Hao Wu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • R

:: DOWNLOAD

 ChIPComp

:: MORE INFORMATION

Citation

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.
Chen L, Wang C, Qin ZS, Wu H.
Bioinformatics. 2015 Feb 13. pii: btv094.

PolyaPeak 0.4 – ChIP-seq Peak Reranking tool using mixture of Multivariate Polya Ditributions

PolyaPeak 0.4

:: DESCRIPTION

PolyaPeak is an R package for ranking ChIP-seq peaks with shape information. polyaPeak uses a Bayesian hierarchical model to incorporate the peak shapes in the ranking. The shapes are described by a mixture of multivariate Polya distributions. Real data analyses show that polyaPeak outperforms several popular peak calling software including MACS, CisGenome and PICS.

::DEVELOPER

Hao Wu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • R

:: DOWNLOAD

 PolyaPeak

:: MORE INFORMATION

Citation

PLoS One. 2014 Mar 7;9(3):e89694. doi: 10.1371/journal.pone.0089694. eCollection 2014.
PolyaPeak: detecting transcription factor binding sites from ChIP-seq using peak shape information.
Wu H1, Ji H

ChIPXpress 1.36.0 – Improve ChIP-seq and ChIP-chip Target Gene Ranking using publicly available Gene Expresison data

ChIPXpress 1.36.0

:: DESCRIPTION

ChIPXpress is a R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data.

::DEVELOPER

George Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

 ChIPXpress

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Jun 10;14:188. doi: 10.1186/1471-2105-14-188.
ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking.
Wu G, Ji H.
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CisGenome 2.0 – ChIP-chip and ChIP-seq Data Analysis

CisGenome 2.0

:: DESCRIPTION

CisGenome is a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data. CisGenome is designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis. In addition to implementing previously published ChIP–microarray (ChIP-chip) analysis methods, the software contains statistical methods designed specifically for ChlP sequencing (ChIP-seq) data obtained by coupling ChIP with massively parallel sequencing. The modular design of CisGenome enables it to support interactive analyses through a graphic user interface as well as customized batch-mode computation for advanced data mining. A built-in browser allows visualization of array images, signals, gene structure, conservation, and DNA sequence and motif information.

::DEVELOPER

Ji Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

CisGenome

:: MORE INFORMATION

Citation

Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers and Wing H.Wong (2008)
An integrated software system for analyzing ChIP-chip and ChIP-seq data.
Nature Biotechnology, 26: 1293-1300. doi:10.1038/nbt.1505

ChIP-Seq 1.5.5 – ChIP-Seq Analysis server

ChIP-Seq 1.5.5

:: DESCRIPTION

The ChIP-Seq Web Server provides access to a set of useful tools performing common ChIP-Seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. Users can analyse their own data by uploading mapped sequence tags in various formats, including BED and BAM. The server also provides access to hundreds of publicly available data sets such as ChIP-seq data, RNA-seq data (i.e. CAGE), DNA-methylation data, sequence annotations (promoters, polyA-sites, etc.), and sequence-derived features (CpG, phastCons scores).

::DEVELOPER

Computational Cancer Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server

:: DOWNLOAD

 ChIP-Seq

:: MORE INFORMATION

DBChIP 1.36.0 – Differential Binding of Transcription Factor with ChIP-seq

DBChIP 1.36.0

:: DESCRIPTION

DBChIP detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples.

::DEVELOPER

Kun Liang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • R
  • BioCOnductor
:: DOWNLOAD

 DBChIP

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 1;28(1):121-2. doi: 10.1093/bioinformatics/btr605. Epub 2011 Nov 3.
Detecting differential binding of transcription factors with ChIP-seq.
Liang K1, Keles S.

ZINBA 2.02.03 – Identifies Genomic Regions Enriched in a Variety of ChIP-seq and DNA-seq

ZINBA 2.02.03

:: DESCRIPTION

ZINBA (Zero-Inflated Negative Binomial Algorithm) is a computational and statistical framework used to call regions of the genome enriched for sequencing reads originating from a diverse array of biological experiments.

::DEVELOPER

ZINBA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 ZINBA

:: MORE INFORMATION

Citation

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions.
Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD.
Genome Biol. 2011 Jul 25;12(7):R67. doi: 10.1186/gb-2011-12-7-r67.