Tag: Resolution

HaploBlock 1.2 – Haplotype Block Identification and Resolution for High-density SNP data.

HaploBlock 1.2

:: DESCRIPTION

HaploBlock is a software program which provides an integrated approach to haplotype block identification, haplotyping SNPs (or haplotype phasing, resolution or reconstruction) and linkage disequilibrium (LD) mapping (or genetic association studies). HaploBlock is suitable for high density haplotype or genotype SNP marker data and is based on a statistical model which takes account of recombination hotspots, bottlenecks, genetic drift and mutations and has a Markov Chain at its core.

::DEVELOPER

Laboratory of Computational Biology , Technion

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 HaploBlock

:: MORE INFORMATION

Citation

G. Greenspan* and D. Geiger
High Density Linkage Disequilibrium Mapping using Models of Haplotype Block Variation
Bioinformatics (2004) 20 (suppl 1): i137-i144.

PrEMeR-CG – Probabilistic Extension of Methylated Reads at CpG resolution

PrEMeR-CG

:: DESCRIPTION

PrEMeR-CG is a computational approach that harnesses the implicit information associated with library fragment profiles to infer nucleotide-resolution methylation values in addition to read counts data.

CpG binning quantifies the methylation for each CpG in the genome using aligned reads and a fragment profile.

::DEVELOPER

Ralf Bundschuh’s Statistical Physics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 PrEMeR-CG

:: MORE INFORMATION

Citation

PrEMeR-CG: Inferring Nucleotide Level DNA Methylation Values from MethylCap-Seq Data.
Frankhouser DE, Murphy M, Blachly JS, Park J, Zoller MW, Ganbat JO, Curfman J, Byrd JC, Lin S, Marcucci G, Yan P, Bundschuh R.
Bioinformatics. 2014 Aug 31. pii: btu583.

ORMAN 1.3 – Optimal Resolution of Ambiguous RNA-Seq Multi-mappings in the Presence of Novel Isoforms

ORMAN 1.3

:: DESCRIPTION

ORMAN ( Optimal Resolution of Multimapping Ambiguity of RNA-Seq Reads) is a tool for resolving multi-mappings within an RNA-Seq SAM file.

::DEVELOPER

Hach Lab

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ORMAN

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 1;30(5):644-51. doi: 10.1093/bioinformatics/btt591. Epub 2013 Oct 15.
ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.
Dao P, Numanagić I, Lin YY, Hach F, Karakoc E, Donmez N, Collins C, Eichler EE, Sahinalp SC.

Vizardous 1.2.0 – Analysis of Microbial Populations with Single Cell Resolution

Vizardous 1.2.0

:: DESCRIPTION

Vizardous is a software for the visualization and evaluation of time-resolved, quantitative, single-cell data.

::DEVELOPER

Modeling & Simulation group at the IBG-1

:: SCREENSHOTS

Vizardous

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 Vizardous

:: MORE INFORMATION

Citation

Vizardous: interactive analysis of microbial populations with single cell resolution.
Helfrich S, Azzouzi CE, Probst C, Seiffarth J, Grünberger A, Wiechert W, Kohlheyer D, Nöh K.
Bioinformatics. 2015 Aug 10. pii: btv468

MMR – Tool for Read Multi-Mapper Resolution

MMR

:: DESCRIPTION

MMR infers optimal mapping locations from the coverage densities of other mapped reads in vicinity.

::DEVELOPER

the Biomedical Informatics Lab of Prof. Dr. Gunnar Rätsch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 MMR

:: MORE INFORMATION

Citation:

MMR: A Tool for Read Multi-Mapper Resolution.
Kahles A, Behr J, Rätsch G.
Bioinformatics. 2015 Oct 30. pii: btv624.

HiCNN 2 – Enhance the Resolution of Hi-C data

HiCNN 2

:: DESCRIPTION

HiCNN is a computational method for resolution enhancement of Hi-C data. It uses a very deep convolutional neural network (54 layers) to learn the mapping between low-resolution and high-resolution Hi-C contact matrices.

HiCNN2 is an improved version of our previously developed tool HiCNN for enhancing resolution of Hi-C data and uses three architectures to learn the mapping between low-resolution and high-resolution Hi-C contact matrices.

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

HiCNN2

:: MORE INFORMATION

Citation

Tong Liu and Zheng Wang.
HiCNN2: Enhancing the Resolution of Hi-C Data Using an Ensemble of Convolutional Neural Networks.
Genes, 2019, 10(11):862.

Tong Liu and Zheng Wang.
HiCNN: A very deep convolutional neural network to better enhance the resolution of Hi-C data.
Bioinformatics, 2019, 35(21):4222-4228.