Tag: Inference

LASSIE – Linear Allele-Specific Selection InferencE

LASSIE

:: DESCRIPTION

ASSIE is a statistical model for inferring selection coefficients associated with coding variants in the human genome.

::DEVELOPER

Siepel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

ASSIE

 :: MORE INFORMATION

Citation

Huang YF, Siepel A.
Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.
Genome Res. 2019 Aug;29(8):1310-1321. doi: 10.1101/gr.245522.118. Epub 2019 Jun 27. PMID: 31249063; PMCID: PMC6673719.

Gist 0.7.17 – Generative Inference of Sequence Taxonomy

Gist 0.7.17

:: DESCRIPTION

Gist began as a project to develop a sequence classifier based on arbitrary input classes, and has developed into a high-precision, noise-tolerant taxonomic classifier focused specifically on the problem of annotating short (76 nt and higher), unassembled reads with little or no quality filtering

::DEVELOPER

Parkinson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Gist

:: MORE INFORMATION

D-GEX 1.01 – Deep Learning for Gene Expression Inference

D-GEX 1.01

:: DESCRIPTION

DGEX is a deep learning method to infer the expression of target genes from the expression of landmark genes.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python

:: DOWNLOAD

 D-GEX

:: MORE INFORMATION

Citation

Gene expression inference with deep learning.
Chen Y, Li Y, Narayan R, Subramanian A, Xie X.
Bioinformatics. 2016 Feb 11. pii: btw074.

HARSH 0.21 – Haplotype Inference using Reference and Sequencing Data

HARSH 0.21

:: DESCRIPTION

HARSH (HAplotype inference using Reference and Sequencing tecHnology) is a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. It is based on a novel probabilistic model and Gibbs sampler method.

::DEVELOPER

ZarLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 HARSH

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 15;29(18):2245-52. doi: 10.1093/bioinformatics/btt386.
Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.
Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E.

PASTRI 0.1 – Probabilistic Algorithm for Somatic TRee Inference

PASTRI 0.1

:: DESCRIPTION

PASTRI is an algorithm that infers tumor phylogenies from one or more bulk DNA sequencing samples.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PASTRI 

:: MORE INFORMATION

Citation:

Satas G, Raphael BJ.
Tumor phylogeny inference using tree-constrained importance sampling.
Bioinformatics. 2017 Jul 15;33(14):i152-i160. doi: 10.1093/bioinformatics/btx270. PMID: 28882002; PMCID: PMC5870673.

DoRIS 0.1 – Demographic Inference based on shared IBD Haplotypes

DoRIS 0.1

:: DESCRIPTION

DoRIS is a Java software tool for demographic inference based on shared IBD haplotypes

::DEVELOPER

Palamara Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Java

:: DOWNLOAD

 DoRIS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):i180-8. doi: 10.1093/bioinformatics/btt239.
Inference of historical migration rates via haplotype sharing.
Palamara PF1, Pe’er I.

FuseNet – Gene Network Inference by Fusing data from Diverse Distributions

FuseNet

:: DESCRIPTION

FuseNet is a Markov network formulation that infers networks from a collection of nonidentically distributed datasets.

::DEVELOPER

FuseNet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 FuseNet

:: MORE INFORMATION

Citation

Gene network inference by fusing data from diverse distributions.
Žitnik M, Zupan B.
Bioinformatics. 2015 Jun 15;31(12):i230-i239. doi: 10.1093/bioinformatics/btv258.

Red – Inference of Epistatic Gene Networks

Red

:: DESCRIPTION

Red is a conceptually new probabilistic approach to gene network inference from quantitative interaction data

::DEVELOPER

BioLab , University of Ljubljana

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Red

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i246-i254. doi: 10.1093/bioinformatics/btu287.
Gene network inference by probabilistic scoring of relationships from a factorized model of interactions.
Zitnik M1, Župan B2.

Ancestor v1.1 – Computational Inference of Ancestral Genomes

Ancestor v1.1

:: DESCRIPTION

Ancestors is a web server allowing one to easily and quickly perform the last three steps of the ancestral genome reconstruction procedure.

::DEVELOPER

Abdoulaye Banire Diallo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jan 1;26(1):130-1. doi: 10.1093/bioinformatics/btp600. Epub 2009 Oct 22.
Ancestors 1.0: a web server for ancestral sequence reconstruction.
Diallo AB1, Makarenkov V, Blanchette M.

Hi-Jack – Pathway-based Inference of Host-pathogen Interactions

Hi-Jack

:: DESCRIPTION

Hi-Jack, a novel computational framework, for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking.

::DEVELOPER

InfoCloud Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Compiler

:: DOWNLOAD

Hi-Jack

:: MORE INFORMATION

Citation:

Hi-Jack: A novel computational framework for pathway-based inference of host-pathogen interactions.
Kleftogiannis D, Wong L, Archer JA, Kalnis P.
Bioinformatics. 2015 Mar 9. pii: btv138

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