MakeHub 1.0.5 – Fully Automated Generation of UCSC Assembly Hubs

MakeHub 1.0.5

:: DESCRIPTION

MakeHub is a command line tool for the fully automatic generation of of track data hubs for visualizing genomes with the UCSC genome browser. Track data hubs are data structures that contain all required information about a genome for visualizing with the UCSC genome browser.

::DEVELOPER

Bioinformatics Greifswald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

MakeHub

:: MORE INFORMATION

Citation

Hoff KJ.
MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs.
Genomics Proteomics Bioinformatics. 2019 Oct;17(5):546-549. doi: 10.1016/j.gpb.2019.05.003. Epub 2020 Jan 28. PMID: 32001327; PMCID: PMC7056914.

HubPredictor v1.0 beta – Predicting Chromatin Interaction Hubs using Histone Marks information

HubPredictor v1.0 beta

:: DESCRIPTION

HubPredictor is the R function to run Bayesian Additive Regression Trees (BART) model for predicting chromatin interaction hubs using histone marks information.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R

:: DOWNLOAD

HubPredictor

:: MORE INFORMATION

Citation

Genome Biol, 16 (1), 162 2015 Aug 14
Predicting Chromatin Organization Using Histone Marks
Jialiang Huang , Eugenio Marco , Luca Pinello , Guo-Cheng Yuan

IMHRC V1 – Inter-Module Hub Removal Clustering

IMHRC V1

:: DESCRIPTION

IMHRC is a graph clustering algorithm that is developed based on inter-module hub removal in the weighted graphs which can detect overlapped clusters. Due to these properties, it is especially useful for detecting protein complexes in protein-protein interaction (PPI) networks with associated confidence values.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Java

:: DOWNLOAD

IMHRC

:: MORE INFORMATION

Citation

Sci Rep. 2017 Jun 12;7(1):3247. doi: 10.1038/s41598-017-03268-w.
Discovering overlapped protein complexes from weighted PPI networks by removing inter-module hubs.
Maddi AMA, Eslahchi C

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