:: DESCRIPTION
DistG counts the length of fasta sequences and make a graphical representation about. There are two king of graphs. The first is the distribution graph, giving an overview of all read fasta files (sequences) so far. The second graph displays a specific file’s counting as a set of rectangles.
::DEVELOPER
Institute of Bioinformatics WWU Muenster
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The DBC software is an alternative method for organizing sequence data into operational taxonomic units (OTUs) for next-generation sequencing technologies, such as Illumina. The focus of this method is to identify sequences that are genetically and ecologically similar to group them, while keeping ecologically distinct organisms apart, regardless of sequence identity.
dbOTU3 is a new implementation of dbOTU that is faster and more user-friendly.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Olesen SW, Duvallet C, Alm EJ.
dbOTU3: A new implementation of distribution-based OTU calling.
PLoS One. 2017 May 4;12(5):e0176335. doi: 10.1371/journal.pone.0176335. PMID: 28472072; PMCID: PMC5417438.
Sarah P. Preheim, Allison R. Perrotta, Antonio M. Martin-Platero, Anika Gupta and Eric J. Alm. 2013.
Distribution-based clustering: Using ecology to refine the operational taxonomic unit.
Appl. Environ. Microbiol. 2013, 79(21):659
:: DESCRIPTION
IDCalc was developed to provide a simple way to view the expected isotope distribution for biological molecules measured by mass spectrometry. The program also includes the the ability to consider enriched stable isotopes.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kubinyi, Analytica Chimica Acta, 247 (1991) 107-119.
The C, H, O, and N isotope abundances are specific to biological molecules
(Dwight E. Matthews personal communication)
:: DESCRIPTION
WORDS VIEWER is a free software which allows to see the distribution of motifs in a group of nucleotide sequences.
::DEVELOPER
Gruppo di Biologia Computazionale
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MPFE is an R Bioconductor package for calculation of the estimated distribution over methylation patterns.
::DEVELOPER
Peijie Lin, Sylvain Foret, Conrad Burden <conrad.burden at anu.edu.au>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Estimation of the methylation pattern distribution from deep sequencing data.
Lin P, Forêt S, Wilson SR, Burden CJ.
BMC Bioinformatics. 2015 May 6;16(1):145.
:: DESCRIPTION
FuseNet is a Markov network formulation that infers networks from a collection of nonidentically distributed datasets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
GMD is an R package to assess the similarity between spatial distributions of read-based sequencing data such as ChIP-seq and RNA-seq. GMD calculates the optimal distance between pairs of normalized signal distributions, optionally sliding one distribution over the other to ‘align’ the distributions. GMD also provides graphical and downstream clustering tools.
::DEVELOPER
Xiaobei Zhao <xiaobei at binf.ku.dk>, Albin Sandelin@The Bioinformatics Centre , University of Copenhagen
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Xiaobei Zhao and Albin Sandelin
GMD: measuring the distance between histograms with applications on high-throughput sequencing reads
Bioinformatics (2012) 28 (8): 1164-1165.
:: DESCRIPTION
The CellOrganizer project provides tools for :learning generative models of cell organization directly from images/ storing and retrieving those models in XML files/ synthesizing cell images (or other representations) from one or more models
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Methods Cell Biol. 2012;110:179-93.
CellOrganizer: Image-derived models of subcellular organization and protein distribution.
Murphy RF.
:: DESCRIPTION
DNC-MIX models the distribution of the gene expression profile of a test sample as a mixture, with each component characterizing the expression levels in a class, and assigns a class label to each test sample
::DEVELOPER
Statistical Genetics and Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Alexandridis, R., Lin, S., Irwin, M. (2004)
Class discovery and classification of tumor samples using mixture modeling of gene expression data.
Bioinformatics, 20, 2545-2552.
:: DESCRIPTION
CENTDIST is a novel web-application for identifying co-localized transcription factors around ChIP-seq peaks. Unlike traditional motif scanning program, CENTDIST does not require any user-specific parameters and the background. It automatically learns the best set of parameters for different motifs and ranks them based on the skewness of their distribution around ChIP-seq peaks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W391-9. doi: 10.1093/nar/gkr387. Epub 2011 May 20.
CENTDIST: discovery of co-associated factors by motif distribution.
Zhang Z1, Chang CW, Goh WL, Sung WK, Cheung E.
