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.

SCENIC 1.1.2 / pySCENIC 0.11.1- Single-cell Regulatory Network Inference and Clustering

SCENIC 1.1.2 / pySCENIC 0.11.1

:: DESCRIPTION

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

::DEVELOPER

aertslab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • R / Python

:: DOWNLOAD

SCENIC / pySCENIC

:: MORE INFORMATION

Citation

Aibar S, et al.
SCENIC: single-cell regulatory network inference and clustering.
Nat Methods. 2017 Nov;14(11):1083-1086. doi: 10.1038/nmeth.4463. Epub 2017 Oct 9. PMID: 28991892; PMCID: PMC5937676.

Van de Sande B,et al.
A scalable SCENIC workflow for single-cell gene regulatory network analysis.
Nat Protoc. 2020 Jul;15(7):2247-2276. doi: 10.1038/s41596-020-0336-2. Epub 2020 Jun 19. PMID: 32561888.

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

ParCorA – Partial Correlation Analysis for the purpose of Biochemical Network Inference

ParCorA

:: DESCRIPTION

ParCorA is a software for partial correlation analysis for the purpose of biochemical network inference from large scale observations, such as obtained with microarrays and metabolic profiling

::DEVELOPER

The Manchester Centre for Integrative Systems Biology(MCISB)

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 ParCorA

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Dec 12;20(18):3565-74. Epub 2004 Jul 29.
Discovery of meaningful associations in genomic data using partial correlation coefficients.
de la Fuente A1, Bing N, Hoeschele I, Mendes P.

StructHDP 1.1 – Inference of number of Clusters and Population Structure from Admixed Genotype data.

StructHDP 1.1

:: DESCRIPTION

StructHDP is a program for automatically inferring the population structure and number of clusters from a sample of admixed genotype data. It extends the model used by Structure to allow for a potentially infinite number of populations and then chooses the number of populations that best explain the data.

::DEVELOPER

Suyash Shringarpure

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 StructHDP

:: MORE INFORMATION

Citation

StructHDP: automatic inference of number of clusters and population structure from admixed genotype data Suyash Shringarpure;
Suyash Shringarpure ,Daegun Won; Eric P. Xing
Bioinformatics 2011 27: i324-i332