BIMr 1.0 – Bayesian Inference of imMigration rates

BIMr 1.0

:: DESCRIPTION

BIMr (Bayesian Inference of imMigration rates) is a free software that makes inferences about recent proportions of immigrant genes in subdivided populations and that identifies the environmental factors that are responsible for observed gene flow patterns.

::DEVELOPER

Laboratoire d’Ecologie Alpine

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOsX

:: DOWNLOAD

BIMr

:: MORE INFORMATION

Citation

Faubet P. and O.E. Gaggiotti, 2008.
A new Bayesian method to identify the environmental factors that influence recent migration.
Genetics 178: 1491–1504.

clonealign 2.0 – Bayesian Inference of clone-specific Gene Expression Estimates

clonealign 2.0

:: DESCRIPTION

clonealign assigns single-cell RNA-seq expression to cancer clones by probabilistically mapping RNA-seq to clone-specific copy number profiles using reparametrization gradient variational inference.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R

:: DOWNLOAD

clonealign

:: MORE INFORMATION

Citation

Genome Biol. 2019 Mar 12;20(1):54. doi: 10.1186/s13059-019-1645-z.
clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers.
Campbell KR, etc.

biRte 1.18.0 – Bayesian Inference of Regulatory Influence on Expression

biRte 1.18.0

:: DESCRIPTION

biRte is an software for bayesian prediction of TF and miRNA activities from different expression data entities; interfaces nem for gene regulatory network inference.

::DEVELOPER

biRte team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R
BioConductor

:: DOWNLOAD

biRte

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jun 25. pii: btv379.
biRte: Bayesian Inference of Context Specific Regulator Activities and Transcriptional Networks.
Fröhlich H

BitSeq 0.7.5 / for R 1.36.0 – Bayesian Inference of Transcripts from Sequencing Data

BitSeq 0.7.5 / for R 1.36.0

:: DESCRIPTION

BitSeq is an application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. An advantage of this approach is the ability to account for both technical uncertainty and intrinsic biological variance in order to avoid false DE calls. The technical contribution to the uncertainty comes both from finite read-depth and the possibly ambiguous mapping of reads to multiple transcripts.

:: DEVELOPER

Peter Glaus , Antti Honkela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / windows/ MacOsX
GCC / BioCOnductor/ R package
Python

:: DOWNLOAD

BitSeq / for R

:: MORE INFORMATION

Citation

Fast and accurate approximate inference of transcript expression from RNA-seq data.
Hensman J, Papastamoulis P, Glaus P, Honkela A, Rattray M.
Bioinformatics. 2015 Aug 26. pii: btv483

Bioinformatics. 2012 Jul 1;28(13):1721-8. doi: 10.1093/bioinformatics/bts260. Epub 2012 May 3.
Identifying differentially expressed transcripts from RNA-seq data with biological variation.
Glaus P, Honkela A, Rattray M.

BIRTA 1.16.0 – Bayesian Inference of Regulation of Transcriptional Activity

BIRTA 1.16.0

:: DESCRIPTION

BIRTA uses the regulatory networks of TFs and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.

::DEVELOPER

Benedikt Zacher <zacher at lmb.uni-muenchen.de>, Holger Froehlich <frohlich at bit.uni-bonn.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R
BioConductor

:: DOWNLOAD

BIRTA

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 1;28(13):1714-20. doi: 10.1093/bioinformatics/bts257. Epub 2012 May 4.
Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data.
Zacher B1, Abnaof K, Gade S, Younesi E, Tresch A, Fr?hlich H.

bcbn 0.02 – Bayesian inference for Conjunctive Bayesian Networks

bcbn 0.02

:: DESCRIPTION

bayes-cbn is an R package including an MCMC sampling algorithm for Bayesian inference of CBNs.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
R package

:: DOWNLOAD

bayes-cbn

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):2318-24. doi: 10.1093/bioinformatics/bts433. Epub 2012 Jul 10.
Efficient sampling for Bayesian inference of conjunctive Bayesian networks.
Sakoparnig T, Beerenwinkel N.

RevBayes 1.0.13 – Bayesian Inference of Phylogeny

RevBayes 1.0.13

:: DESCRIPTION

RevBayes provides an R-like environment for evolutionary analysis using Bayesian inference and graphical models

::DEVELOPER

RevBayes team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX / Windows

:: DOWNLOAD

RevBayes

:: MORE INFORMATION

Citation

Höhna, S., Heath, T. A., Boussau, B., Landis, M. J., Ronquist, F., Huelsenbeck, J. P. (2014).
Probabilistic graphical model representation in phylogenetics.
Systematic Biology 63:753–771.

BayesAssNM 1.0 – Bayesian Inference of Recent Migration Using Multilocus Genotypes (Migrants Not Included In the Sample)

BayesAssNM 1.0

:: DESCRIPTION

BayesAssNM is a program that estimates recent migration rates between populations using MCMC.

::DEVELOPER

Rannala Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

BayesAssNM

:: MORE INFORMATION

Citation

Jehle R, GA Wilson, JW Arntzen, and T Burke. 2005.
Contemporary gene flow and the spatio-temporal genetic structure of subdivided newt populations (Triturus cristatus, T. marmoratus).
J Evol Biol. 2005 May;18(3):619-28.

BayesAss 3.03 -Bayesian Inference of Recent Migration Using Multilocus Genotype

BayesAss 3.03

:: DESCRIPTION

BayesAss is a software that uses individual multilocus genotypes to estimate rates of recent immigration (over the last several generations) among populations is presented. The software also estimates the posterior probability distributions of individual immigrant ancestries, population allele frequencies, population inbreeding coefficients, and other parameters of potential interest.

::DEVELOPER

Rannala Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

BayesAss

:: MORE INFORMATION

Citation

G.A. Wilson and B. Rannala 2003.
Bayesian inference of recent migration rates using multilocus genotypes.
Genetics 163: 1177-1191.

PhyBayes 200208 – Bayesian Inference in Phylogenetics

PhyBayes 200208

:: DESCRIPTION

PhyBayes is a program for Bayesian inference in phylogenetics

– estimation of divergence dates / rates of molecular evolution
– Bayes factor and test of evolutionary hypotheses
– tree space search and estimation of the posterior probabilities
– estimation of heterogeneities in a data set (still a project…)

::DEVELOPER

The Aris-Brosou lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / DOS

:: DOWNLOAD

PhyBayes

:: MORE INFORMATION

Citaion

Aris-Brosou, S. and Z. Yang. 2002.
The effects of models of rate evolution on estimation of divergence dates with a special reference to the metazoan 18S rRNA phylogeny.
Syst. Biol. 51:703-714.