Tag: Chromatin

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.

MCMC5C – Prediction of Chromatin 3D Structure

MCMC5C

:: DESCRIPTION

MCMC5C is a probabilistic model linking 5C/Hi-C data to physical distances and describe a Markov chain Monte Carlo (MCMC) approach to generate a representative sample from the posterior distribution over structures from IF data.

::DEVELOPER

Dr. Josée Dostie Lab

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 MCMC5C

:: MORE INFORMATION

Citation

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling.
Rousseau M, Fraser J, Ferraiuolo MA, Dostie J, Blanchette M.
BMC Bioinformatics. 2011 Oct 25;12:414. doi: 10.1186/1471-2105-12-414.

Chromatin Cutter 1.00 – Simulates the distribution of DNA in a Gel Electrophoresis Study of Yeast Chromatin cut by Enzymes

Chromatin Cutter 1.00

:: DESCRIPTION

Chromatin Cutter simulates the distribution of DNA in a gel electrophoresis study of Yeast chromatin cut by enzymes. It lets you specify the fraction of nucleosomes that are unwrapped (wrapped ones have inaccessible DNA). It lets you specify the variance in the distribution of nucleosomes around their mean distance. It lets you specify the number of cuts per unit length (enzyme concentration). It plots the effects of these on the log number of base pairs, which matches the gel electrophoresis mass distribution.

::DEVELOPER

CISMM (Computer Integrated Systems for Microscopy and Manipulation)

:: SCREENSHOTS

ChromatinCutter

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Chromatin Cutter

:: MORE INFORMATION

ArchAlign 1.5 – Chromatin Alignment Algorithm for Detecting Chromatin Architecture

ArchAlign 1.5

:: DESCRIPTION

ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets, derived from next-generation sequencing or tiled microarray approaches, by aligning chromatin signals for regions of interest.

::DEVELOPER

Buck Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ArchAlign

:: MORE INFORMATION

Citation:

Genome Biol. 2010;11(12):R126. doi: 10.1186/gb-2010-11-12-r126. Epub 2010 Dec 23.
ArchAlign: coordinate-free chromatin alignment reveals novel architectures.
Lai WK1, Buck MJ.

HubPredictor v1.0 beta – Predicting Chromatin Interaction Hubs using Histone Marks information

HubPredictor v1.0 beta

:: DESCRIPTION

HubPredictor is the R function to run Bayesian Additive Regression Trees (BART) model for predicting chromatin interaction hubs using histone marks information.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R

:: DOWNLOAD

HubPredictor

:: MORE INFORMATION

Citation

Genome Biol, 16 (1), 162 2015 Aug 14
Predicting Chromatin Organization Using Histone Marks
Jialiang Huang , Eugenio Marco , Luca Pinello , Guo-Cheng Yuan

diHMM v0.1 beta – multi-scale Chromatin State Annotation from ChIPseq data

diHMM v0.1 beta

:: DESCRIPTION

diHMM (Hierarchical Hidden Markov Model) is a novel computational method for finding chromatin states at multiple scales. The model takes as input a multidimensional set of histone modifications for several cell types and classifies the genome into a preselected number of nucleosome-level and domain-level hidden states.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Matlab

:: DOWNLOAD

diHMM

:: MORE INFORMATION

Citation

Marco E, Meuleman W, Huang J, Glass K, Pinello L, Wang J, Kellis M, Yuan GC.
Multi-scale chromatin state annotation using a hierarchical hidden Markov model.
Nature Communications. 2017 Apr 7;8:15011.

AutoChrom3D v1 – Modeling and Visualization the 3D Structure of Human or Mouse Chromatin

AutoChrom3D v1

:: DESCRIPTION

AutoChrom3D was built for modeling and visualization the 3D structure of human or mouse chromatin. The 3D structure of chromatin is calculated and generated based on HiC data.

::DEVELOPER

PENG Cheng (email: pengcheng@mail.hzau.edu.cn).

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl
:: DOWNLOAD

  AutoChrom3D 

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Oct;41(19):e183. doi: 10.1093/nar/gkt745. Epub 2013 Aug 21.
The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling.
Peng C1, Fu LY, Dong PF, Deng ZL, Li JX, Wang XT, Zhang HY.

tREX – Reconstruction of 3D structure of Chromatins using Hi-C data

tREX

:: DESCRIPTION

tPAM and tREX(truncated Random effect EXpression) are codes for reconstruction of 3D structure of chromatins using Hi-C data based on two model-based algorithms.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

tREX

:: MORE INFORMATION

Citation

BMC Bioinformatics, 17, 70 2016 Feb 6
Impact of Data Resolution on Three-Dimensional Structure Inference Methods
Jincheol Park, Shili Lin

InfMod3DGen – Inferential Modeling of 3D Chromatin Structure

InfMod3DGen

:: DESCRIPTION

InfMod3DGen is a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data.

::DEVELOPER

InfMod3DGen team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 InfMod3DGen

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Apr 30;43(8):e54. doi: 10.1093/nar/gkv100.
Inferential modeling of 3D chromatin structure.
Wang S, Xu J, Zeng J.

ChromaSig – Find Common Chromatin Signatures

ChromaSig

:: DESCRIPTION

ChromaSig is an unsupervised learning method, which finds, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data.

::DEVELOPER

Ren Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ChromaSig

:: MORE INFORMATION

Citation

Gary Hon, Bing Ren, Wei Wang
ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome
PLoS Comput Biol 4(10): e1000201.