Tag: Multiple Loci

BPrimm 1.12 – Bayesian and Penalized Regression in Multiple Loci Mapping

BPrimm 1.12

:: DESCRIPTION

BPrimm (Bayesian and Penalized regression in multiple loci mapping) includes a set of tools for simultaneously multiple loci mapping, and two novel methods named the Bayesian adaptive Lasso and the Iterative Adaptive Lasso

::DEVELOPER

Wei Sun

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 BPrimm

:: MORE INFORMATION

Citation

Wei Sun, Joseph G. Ibrahim and Fei Zou
Genome-wide Multiple Loci Mapping in Experimental Crosses by the Iterative Adaptive Penalized Regression
Genetics May 2010 vol. 185 no. 1 349-359

C-State 0.2.3 – Query and Plot Chromatin Landscapes across multiple loci and Cell Types

C-State 0.2.3

:: DESCRIPTION

C-State (Chromatin-State) is an interactive platform that enables experimentalists who lack bioinformatics support to investigate epigenetic landscapes across multiple datasets for comparative epigenomic analysis.

::DEVELOPER

Rakesh Mishra Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX

:: DOWNLOAD

C-State

:: MORE INFORMATION

Citation:

Sowpati DT, Srivastava S, Dhawan J, Mishra RK.
C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search.
BMC Bioinformatics. 2017 Sep 13;18(Suppl 10):392. doi: 10.1186/s12859-017-1786-6. PMID: 28929968; PMCID: PMC5606219.

MuMRescueLite 20090522 – Use the Tag Sequencies of mapped to Multiple Loci to the Genome

MuMRescueLite 20090522

:: DESCRIPTION

MuMRescueLite is the software that enable to use the tag sequencies of mapped to multiple loci to the genome, for the expression analysis. At the mapping of short sequence tags of CAGE or ChIP-Seq to the genome, sequence tags that map to multiple genomic loci (multi-mapping tags or MuMs), are routinely omitted from further analysis, leading to experimental bias and reduced coverage.

::DEVELOPER

Takehiro Hashimoto, Michiel J. L. deHoon, Geoffrey J. Faulkner

:: SCREENSHOTS

N/A

::  REQUIREMENTS

  • Linux / MacOSX / Windows
  • Python

:: DOWNLOAD

  MuMRescueLite

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Oct 1;25(19):2613-4. Epub 2009 Jul 15.
Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.
Hashimoto T, de Hoon MJ, Grimmond SM, Daub CO, Hayashizaki Y, Faulkner GJ.