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.

ChAsE 1.0.11 – Chromatin analysis and exploration tool

ChAsE 1.0.11

:: DESCRIPTION

ChAsE is a cross-platform desktop application developed for interactive visualization, exploration and clustering of epigenomic data such as ChIP-seq experiments.

::DEVELOPER

ChAsE team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX/ Linux
  • Java

:: DOWNLOAD

 ChAsE

:: MORE INFORMATION

Citation

ChAsE: Chromatin analysis and exploration tool.
Younesy H, Nielsen CB, Lorincz MC, Jones SJ, Karimi MM, Möller T.
Bioinformatics. 2016 Jul 4. pii: btw382.

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.

diffReps 1.55.4 – Finding Differential Chromatin Modification Sites from ChIP-seq data

diffReps 1.55.4

:: 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.

dCMA – differential Chromatin Modification Analysis

dCMA

:: DESCRIPTION

dCMA is a package for identifying cell-type specific genomic regions with distinctive chromatin modifications.

::DEVELOPER

Shihua Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 dCMA

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Nov;41(20):9230-42. doi: 10.1093/nar/gkt712. Epub 2013 Aug 14.
Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis.
Chen C1, Zhang S, Zhang XS.

msCentipede 1.0 – Hierarchical Multiscale model for inferring Transcription Factor Binding from Chromatin Accessibility data

msCentipede 1.0

:: DESCRIPTION

msCentipede is an algorithm for accurately inferring transcription factor binding sites using chromatin accessibility data (Dnase-seq, ATAC-seq)

::DEVELOPER

Anil Raj

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Python

:: DOWNLOAD

 msCentipede

:: MORE INFORMATION

Citation

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding.
Raj A, Shim H, Gilad Y, Pritchard JK, Stephens M.
PLoS One. 2015 Sep 25;10(9):e0138030. doi: 10.1371/journal.pone.0138030.