HaMMLET – Fast Bayesian Hidden Markov Model with Wavelet Compression

HaMMLET

:: DESCRIPTION

HaMMLET is a fast Forward-Backward Gibbs sampler for Bayesian inference on Hidden Markov Models (HMM). It uses the Haar wavelet transform to dynamically compress the data based on the current variance sample in each iteration.

::DEVELOPER

Schliep lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 HaMMLET

:: MORE INFORMATION

Citation

Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression.
Wiedenhoeft J, Brugel E, Schliep A.
PLoS Comput Biol. 2016 May 13;12(5):e1004871. doi: 10.1371/journal.pcbi.1004871.

XMRF 1.0 – Fit Markov Networks to High-Throughput Genomics Data

XMRF 1.0

:: DESCRIPTION

XMRF is an R package implemented to enable biomedical researchers to discover complex interaction between genes from multi-dimensional genomics data.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

XMRF

:: MORE INFORMATION

Citation

Wan YW, Allen GI, Baker Y, Yang E, Ravikumar P, Anderson M, Liu Z.
XMRF: an R package to fit Markov Networks to high-throughput genetics data.
BMC Syst Biol. 2016 Aug 26;10 Suppl 3(Suppl 3):69. doi: 10.1186/s12918-016-0313-0. PMID: 27586041; PMCID: PMC5009817.

MAPSD – Markov Affinity-based Proteogenomic Signal Diffusion

MAPSD

:: DESCRIPTION

MAPSD is a multi-omic signal diffusion algorithm designed to identify the disease susceptibility scores in unknown genes (or proteins) in complex and polygenic diseases such as schizophrenia.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

MAPSD

:: MORE INFORMATION

Citation

Doostparast Torshizi A, Duan J, Wang K.
Cell type-specific proteogenomic signal diffusion for integrating multi-omics data predicts novel schizophrenia risk genes.
bioRxiv, 2020.

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