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A multiple testing procedure for multi-dimensional pairwise comparisons with ...
Background Often researchers are interested in comparing multiple experimental groups (e.g. tumor size) with a reference group (e.g. normal tissue) on the basis of thousands of... -
Joint use of over- and under-sampling techniques and cross-validation for the...
Background Prediction models are used in clinical research to develop rules that can be used to accurately predict the outcome of the patients based on some of their... -
Bioinformatics identification of new targets for improving low temperature st...
Background Phenotypic studies in Triticeae have shown that low temperature-induced protective mechanisms are developmentally regulated and involve dynamic acclimation processes.... -
Exact p-values for pairwise comparison of Friedman rank sums, with applicatio...
Background The Friedman rank sum test is a widely-used nonparametric method in computational biology. In addition to examining the overall null hypothesis of no significant... -
Combining location-and-scale batch effect adjustment with data cleaning by la...
Background In the context of high-throughput molecular data analysis it is common that the observations included in a dataset form distinct groups; for example, measured at... -
TCGA2BED: Extracting, extending, integrating, and querying The Cancer Genome ...
Background Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical... -
SoftPanel: a website for grouping diseases and related disorders for generati...
Background Targeted next-generation sequencing is playing an increasingly important role in biological research and clinical diagnosis by allowing researchers to sequence high... -
EchinoDB, an application for comparative transcriptomics of deeply-sampled cl...
Background One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation... -
A fast exact sequential algorithm for the partial digest problem
Background Restriction site analysis involves determining the locations of restriction sites after the process of digestion by reconstructing their positions based on the... -
A decision analysis model for KEGG pathway analysis
Background The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis... -
Drug-target interaction prediction via class imbalance-aware ensemble learning
Background Multiple computational methods for predicting drug-target interactions have been developed to facilitate the drug discovery process. These methods use available data... -
IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRN...
Background The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via the sequencing of phylogenetic marker genes (e.g. 16S... -
Evaluation of logistic regression models and effect of covariates for case–co...
Background Next generation sequencing provides a count of RNA molecules in the form of short reads, yielding discrete, often highly non-normally distributed gene expression... -
CytoSpectre: a tool for spectral analysis of oriented structures on cellular ...
Background Orientation and the degree of isotropy are important in many biological systems such as the sarcomeres of cardiomyocytes and other fibrillar structures of the... -
Towards a phenome-wide catalog of human clinical traits impacted by genetic a...
Background Racial/ethnic differences for commonly measured clinical variables are well documented, and it has been postulated that population-specific genetic factors may play a... -
ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publica...
Background Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to... -
SnoReport 2.0: new features and a refined Support Vector Machine to improve s...
Background snoReport uses RNA secondary structure prediction combined with machine learning as the basis to identify the two main classes of small nucleolar RNAs, the box H/ACA... -
AutoSOME: a clustering method for identifying gene expression modules without...
Abstract Background Clustering the information content of large high-dimensional gene expression datasets has widespread application in "omics" biology. Unfortunately, the... -
"CellProfiler Tracer: exploring and validating high-throughput, time-lapse mi...
Background Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been... -
An Eigenvalue test for spatial principal component analysis
AbstractBackgroundThe spatial Principal Component Analysis (sPCA, Jombart 2008) is designed to investigate non-random spatial distributions of genetic variation. Unfortunately,...
