Tag: Bayesian

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

bach

:: 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.

Dizzy-Beats 20150113 – Systems Biology Computing the Bayesian Evidence and parameter posteriors for Systems Models

Dizzy-Beats 20150113

:: DESCRIPTION

Dizzy-Beats is a graphical Java application that builds on the established Dizzy simulator

::DEVELOPER

Dr Stuart Aitken

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Dizzy-Beats

:: MORE INFORMATION

Citation:

Dizzy-Beats: a Bayesian Evidence analysis tool for systems biology.
Aitken S, Kilpatrick AM, Akman OE.
Bioinformatics. 2015 Jan 30. pii: btv062.

BhGLM 1.1.1 – Bayesian hierarchical GLMs to Genetic Data Analysis

BhGLM 1.1.1

:: DESCRIPTION

BhGLM (Bayesian hierarchical GLMs) is an R package. This package provides functions for setting up and fitting Bayesian hierarchical GLMs, for numerically and graphically displaying the results, and for genetic association studies and QTL mapping. The Bayesian hierarchical GLMs include many models as special cases, e.g., classical GLMs, ridge regression, Bayesian lasso, and various adaptive lasso. These methods can be used not only for general data analysis but also for high-dimensional and correlated data. The functions are particularly useful for complicated genetic data analysis, for example, QTL mapping in experimental crosses, genetic association studies for rare and common variants, prediction of complex diseases and traits, gene-set and pathway analysis, and gene-gene and gene-environment interactions.

::DEVELOPER

Nengjun Yi, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BhGLM

:: MORE INFORMATION

Citation

PLoS Genet. 2011 Dec;7(12):e1002382. doi: 10.1371/journal.pgen.1002382. Epub 2011 Dec 1.
Hierarchical generalized linear models for multiple groups of rare and common variants: jointly estimating group and individual-variant effects.
Yi N1, Liu N, Zhi D, Li J.

BLR 1.6 / BGLR 1.0.8 – Bayesian Linear Regression

BLR 1.6 / BGLR 1.0.8

:: DESCRIPTION

BLR (Bayesian Linear Regression) was designed to fit parametric regression models using different types of shrinkage methods. Linear regression with high-dimensional predictors (e.g. SNP) and pedigree.

BGLR: Bayesian Generalized Linear Regression

::DEVELOPER

Paulino Perez Rodriguez <perpdgo at colpos.mx>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BLR / BGLR

:: MORE INFORMATION

Citation:

Gustavo de los Campos, Hugo Naya , Daniel Gianola , José Crossa , Andrés Legarra , Eduardo Manfredi , Kent Weigel and José Miguel Cotes
Predicting Quantitative Traits With Regression Models for Dense Molecular Markers and Pedigree.
Genetics. 182;375-385, 2009. (doi:10.1534/genetics.109.101501)

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.

RP-BP 2.0.0 – Ribosome Profiling with Bayesian Predictions

RP-BP 2.0.0

:: DESCRIPTION

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

Rp-Bp

:: MORE INFORMATION

Citation

Malone B, Atanassov I, Aeschimann F, Li X, Großhans H, Dieterich C.
Bayesian prediction of RNA translation from ribosome profiling.
Nucleic Acids Res. 2017 Apr 7;45(6):2960-2972. doi: 10.1093/nar/gkw1350. PMID: 28126919; PMCID: PMC5389577.

BAli-Phy 3.6.0 – Bayesian Alignment and Phylogeny estimation

BAli-Phy 3.6.0

:: DESCRIPTION

BAli-Phy is MCMC software for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters).BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy accounts for alignment uncertainty by integrating over all alignments. BAli-Phy does not rely on a guide tree because the alignment and the tree are co-estimated. Therefore it can construct phylogeny estimates of widely divergent sequences without bias toward a guide tree.

::DEVELOPER

BAli-Phy team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows

:: DOWNLOAD

 BAli-Phy

:: MORE INFORMATION

Citation

Suchard MA and Redelings BD
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny,
Bioinformatics, 22:2047-2048, 2006.

BUCKy 1.4.4 – Gene Tree Reconciliation with Bayesian Concordance Analysis

BUCKy 1.4.4

:: DESCRIPTION

BUCKy (Bayesian Untangling of Concordance Knots) is a free program that implements Bayesian concordance analysis. The method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes. A population tree with branch lengths in coalescent units is estimated from quartet concordance factors. BUCKy estimates the dominant history of sampled individuals, and how much of the genome supports each relationship, using Bayesian concordance analysis. BUCKy does not assume that genes (or loci) all have the same topology. Instead, groups of genes sharing the same tree are detected (while accounting for uncertainty in gene tree estimates), and then combined to gain more resolution on their common tree. No assumption is made regarding the reason for discordance among gene trees.

::DEVELOPER

Cécile Ané & Bret Larget

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • C++ Compiler

:: DOWNLOAD

BUCKy

:: MORE INFORMATION

Citation

B. Larget, S.K. Kotha, C.N. Dewey, C. Ané (2010).
BUCKy: Gene tree / species tree reconciliation with the Bayesian concordance analysis.
Bioinformatics (2010) September 21, 2010 doi: 10.1093/bioinformatics/btq539

RDP Classifier 2.13 – Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

RDP Classifier 2.13

:: DESCRIPTION

The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment

::DEVELOPER

The Ribosomal Database Project 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX /Windows
  • Java

:: DOWNLOAD

 RDP Classifier

:: MORE INFORMATION

Citation

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.
Wang Q, Garrity GM, Tiedje JM, Cole JR.
Appl Environ Microbiol. 2007 Aug;73(16):5261-7. Epub 2007 Jun 22.

DGEclust 20171006 – Hierarchical non-parametric Bayesian Clustering of Digital Expression data

DGEclust 20171006

:: DESCRIPTION

DGEclust is a program for clustering and differential expression analysis of expression data generated by next-generation sequencing assays, such as RNA-seq, CAGE and others.

::DEVELOPER

Dimitris Vavoulis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DGEclust 

:: MORE INFORMATION

Citation:

Genome Biol. 2015 Feb 20;16:39. doi: 10.1186/s13059-015-0604-6.
DGEclust: differential expression analysis of clustered count data.
Vavoulis DV, Francescatto M, Heutink P, Gough J.

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