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bioconductor-targetsearch
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public |
A package for the analysis of GC-MS metabolite profiling data
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2024-12-15 |
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bioconductor-panr
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public |
Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations
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2024-12-15 |
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bioconductor-switchbox
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public |
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
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2024-12-15 |
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bioconductor-nupop
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public |
An R package for nucleosome positioning prediction
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2024-12-15 |
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bioconductor-santa
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public |
Spatial Analysis of Network Associations
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2024-12-15 |
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r-phylomeasures
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public |
Given a phylogenetic tree T and an assemblage S of species represented as a subset of tips in T, we want to compute a measure of the diversity of the species in S with respect to T. The current package offers efficient algorithms that can process large phylogenetic data for several such measures. Most importantly, the package includes algorithms for computing efficiently the standardized versions of phylogenetic measures and their p-values, which are essential for null model comparisons. Among other functions, the package provides efficient computation of richness-standardized versions for indices such as the net relatedness index (NRI), nearest taxon index (NTI), phylogenetic diversity index (PDI), and the corresponding indices of two-sample measures. The package also introduces a new single-sample measure, the Core Ancestor Cost (CAC); the package provides functions for computing the value and the standardised index of the CAC and, more than that, there is an extra function available that can compute exactly any statistical moment of the measure. The package supports computations under different null models, including abundance-weighted models.
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2024-12-15 |
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bioconductor-biocneighbors
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public |
Nearest Neighbor Detection for Bioconductor Packages
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2024-12-15 |
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bioconductor-lfa
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public |
Logistic Factor Analysis for Categorical Data
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2024-12-15 |
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bioconductor-linnorm
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public |
Linear model and normality based normalization and transformation method (Linnorm)
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2024-12-15 |
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bioconductor-oscope
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public |
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
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2024-12-15 |
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bioconductor-emdomics
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public |
Earth Mover's Distance for Differential Analysis of Genomics Data
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2024-12-15 |
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bioconductor-bus
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public |
Gene network reconstruction
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2024-12-15 |
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bioconductor-pcan
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public |
Phenotype Consensus ANalysis (PCAN)
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2024-12-15 |
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bioconductor-dcgsa
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public |
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
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2024-12-15 |
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bioconductor-mixomics
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public |
Omics Data Integration Project
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2024-12-15 |
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bioconductor-abseqr
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public |
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
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2024-12-15 |
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bioconductor-synlet
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public |
Hits Selection for Synthetic Lethal RNAi Screen Data
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2024-12-14 |
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bioconductor-desingle
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public |
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
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2024-12-14 |
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bioconductor-compass
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public |
Combinatorial Polyfunctionality Analysis of Single Cells
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2024-12-14 |
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bioconductor-kinswingr
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public |
KinSwingR: network-based kinase activity prediction
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2024-12-14 |
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bioconductor-mbcb
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public |
MBCB (Model-based Background Correction for Beadarray)
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2024-12-14 |
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bioconductor-ctsge
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public |
Clustering of Time Series Gene Expression data
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2024-12-14 |
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bioconductor-absseq
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public |
ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
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2024-12-14 |
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bioconductor-massspecwavelet
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public |
Peak Detection for Mass Spectrometry data using wavelet-based algorithms
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2024-12-14 |
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bioconductor-qubic
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public |
An R package for qualitative biclustering in support of gene co-expression analyses
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2024-12-14 |
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r-pscbs
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public |
Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
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2024-12-14 |
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r-metama
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public |
Combines either p-values or modified effect sizes from different studies to find differentially expressed genes
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2024-12-14 |
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bioconductor-minet
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public |
Mutual Information NETworks
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2024-12-14 |
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bioconductor-deqms
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public |
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
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2024-12-14 |
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bioconductor-marray
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public |
Exploratory analysis for two-color spotted microarray data
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2024-12-14 |
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bioconductor-ichip
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public |
Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
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2024-12-14 |
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bioconductor-methylmix
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public |
MethylMix: Identifying methylation driven cancer genes
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2024-12-14 |
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bioconductor-limmagui
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public |
GUI for limma Package With Two Color Microarrays
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2024-12-14 |
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bioconductor-rprotobuflib
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public |
C++ headers and static libraries of Protocol buffers
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2024-12-14 |
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bioconductor-stattarget
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public |
Statistical Analysis of Molecular Profiles
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2024-12-14 |
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bioconductor-multiclust
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public |
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
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2024-12-14 |
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bioconductor-icobra
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public |
Comparison and Visualization of Ranking and Assignment Methods
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2024-12-14 |
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r-speaq
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public |
Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in 'speaq' or available elsewhere on CRAN. More detail can be found in Vu et al. (2011) <doi:10.1186/1471-2105-12-405> and Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018>.
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2024-12-14 |
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bioconductor-edger
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public |
Empirical Analysis of Digital Gene Expression Data in R
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2024-12-14 |
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r-swamp
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public |
Collection of functions to connect the structure of the data with the information on the samples. Three types of associations are covered: 1. linear model of principal components. 2. hierarchical clustering analysis. 3. distribution of features-sample annotation associations. Additionally, the inter-relation between sample annotations can be analyzed. Simple methods are provided for the correction of batch effects and removal of principal components.
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2024-12-14 |
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bioconductor-levi
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public |
Landscape Expression Visualization Interface
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2024-12-14 |
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r-ic10
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public |
Implementation of the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group.
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2024-12-14 |
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bioconductor-wrench
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public |
Wrench normalization for sparse count data
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2024-12-14 |
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bioconductor-tkwidgets
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public |
R based tk widgets
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2024-12-14 |
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bioconductor-samspectral
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public |
Identifies cell population in flow cytometry data
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2024-12-14 |
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bioconductor-beaddatapackr
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public |
Compression of Illumina BeadArray data
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2024-12-14 |
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bioconductor-intramirexplorer
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public |
Predicting Targets for Drosophila Intragenic miRNAs
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2024-12-14 |
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bioconductor-biocworkflowtools
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public |
Tools to aid the development of Bioconductor Workflow packages
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2024-12-14 |
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bioconductor-illuminaio
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public |
Parsing Illumina Microarray Output Files
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2024-12-14 |
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bioconductor-process
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public |
Ciphergen SELDI-TOF Processing
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2024-12-14 |
