Selfish – Discovery of Differential Chromatin Interactions via a Self-Similarity Measure

Selfish

:: DESCRIPTION

SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps. It uses self-similarity to model interactions in a robust way.

::DEVELOPER

Lonardi Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Matlab

:: DOWNLOAD

SELFISH

:: MORE INFORMATION

Citation

Ardakany AR, Ay F, Lonardi S.
Selfish: discovery of differential chromatin interactions via a self-similarity measure.
Bioinformatics. 2019 Jul 15;35(14):i145-i153. doi: 10.1093/bioinformatics/btz362. PMID: 31510653; PMCID: PMC6612869.

C-State 0.2.3 – Query and Plot Chromatin Landscapes across multiple loci and Cell Types

C-State 0.2.3

:: DESCRIPTION

C-State (Chromatin-State) is an interactive platform that enables experimentalists who lack bioinformatics support to investigate epigenetic landscapes across multiple datasets for comparative epigenomic analysis.

::DEVELOPER

Rakesh Mishra Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows /MacOsX

:: DOWNLOAD

C-State

:: MORE INFORMATION

Citation:

Sowpati DT, Srivastava S, Dhawan J, Mishra RK.
C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search.
BMC Bioinformatics. 2017 Sep 13;18(Suppl 10):392. doi: 10.1186/s12859-017-1786-6. PMID: 28929968; PMCID: PMC5606219.

cdBEST – Chromatin Domain Boundary Element Search Tool

cdBEST

:: DESCRIPTION

cdBEST is a tool/software developed in Perl to search the chromatin domain boundary element sequences in 12 Drosophila species. cdBEST uses recognition sequences of boundary interacting proteins and looks for ‘motif clusters’ under a set of constrains to predict boundary element sequences. Apart from Drosophila, cdBEST can be used in several other insect genomes, where the boundary interacting proteins are conserved.

::DEVELOPER

Rakesh Mishra Lab

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows /MacOsX
Perl

:: DOWNLOAD

cdBEST

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 May;40(10):4385-95. doi: 10.1093/nar/gks045. Epub 2012 Jan 28.
Chromatin domain boundary element search tool for Drosophila.
Srinivasan A1, Mishra RK.

BACH / BACH-MIX – Bayesian 3D constructor for Hi-C data / Characterize Structural Variations of Chromatin Folding

BACH / BACH-MIX

:: DESCRIPTION

BACH is a novel Bayesian probabilistic approach for analyzing Hi-C data. BACH takes the Hi-C contact matrix and local genomic features (restriction enzyme cutting frequencies, GC content and sequence uniqueness) as input and produces, via MCMC computation, the posterior distribution of three-dimensional (3D) chromosomal structure

BACH-MIX is an extended BACH algorithm to characterize structural variations of chromatin folding

::DEVELOPER

Jun Liu

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux
R

:: DOWNLOAD

BACH , BACH-MIX

:: MORE INFORMATION

Citation

Hu M, Deng K, Qin Z, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. (2013)
Bayesian Inference of Spatial Organizations of Chromosomes.
PLoS Computational Biology 9(1): e1002893.

CSMinFinder – Chromatin State with Minimum length Finder

CSMinFinder

:: DESCRIPTION

CSMinFinder is a linear time algorithm for calculating a set of non-overlapping regions that maximizes the sum of similarities between the vector of focal epigenetic states and the vectors of raw epigenetic states at DNA positions in the set of regions.

::DEVELOPER

Morishita Laboratory, the University of Tokyo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
C++ Compiler

:: DOWNLOAD

CSMinFinder

:: MORE INFORMATION

Citation

A linear time algorithm for detecting long genomic regions enriched with a specific combination of epigenetic states.
Ichikawa K, Morishita S.
BMC Genomics. 2015;16 Suppl 2:S8. doi: 10.1186/1471-2164-16-S2-S8

hiHMM – Bayesian non-parametric joint inference of Chromatin State Maps

hiHMM

:: DESCRIPTION

hiHMM (hierarchically-linked infinite hidden Markov model) is a new Bayesian non-parametric method to jointly infer chromatin state maps in multiple genomes (different cell types, developmental stages, even multiple species) using genome-wide histone modification data.

::DEVELOPER

SNUBI (Snubi’s Not Unics, Biomedical Informatics.)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux
MatLab/ R

:: DOWNLOAD

hiHMM

:: MORE INFORMATION

Citation:

hiHMM: Bayesian non-parametric joint inference of chromatin state maps.
Sohn KA, Ho JW, Djordjevic D, Jeong HH, Park PJ, Kim JH.
Bioinformatics. 2015 Feb 27. pii: btv117.

Spectacle 1.4 – Spectral learning for Annotating Chromatin Labels and Epigenomes

Spectacle 1.4

:: DESCRIPTION

Spectacle impelements a spectral learning algorithm for hidden Markov models for epigenomic data.

::DEVELOPER

Kevin Chen’s group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows
Java
Python

:: DOWNLOAD

Spectacle

:: MORE INFORMATION

Citation:

Genome Biol. 2015 Feb 12;16(1):33. doi: 10.1186/s13059-015-0598-0.
Spectacle: fast chromatin state annotation using spectral learning.
Song J, Chen KC.

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.

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.

GenomicInteractions 1.26.0 – Exploring Chromatin interaction data

GenomicInteractions 1.26.0

:: DESCRIPTION

GenomicInteractions is an R/Bioconductor package for manipulating and investigating chromatin interaction data.

::DEVELOPER

Computational Regulatory Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R/Bioconductor

:: DOWNLOAD

GenomicInteractions

:: MORE INFORMATION

Citation:

Harmston N, Ing-Simmons E, Perry M, Barešić A, Lenhard B.
GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data.
BMC Genomics. 2015 Nov 17;16:963. doi: 10.1186/s12864-015-2140-x. PMID: 26576536; PMCID: PMC4650858.