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  1. seqinr                

    Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Seqinr includes utilities for sequence data management under the ACNUC system d...

  2. bios2mds

    Bios2mds is primarily dedicated to the analysis of biological sequences by metric MultiDimensional Scaling with projection of supplementary data. It contains functions for readi...

  3. bbo                     

    This package provides an R implementation of Biogeography-Based Optimization (BBO), originally invented by Prof. Dan Simon, Cleveland State University, Ohio. This method is an a...

  4. sybil                

    This Systems Biology Package (Gelius-Dietrich et. al. (2012) ) implements algorithms for constraint based analyses of metabolic networks, e.g. flux-...

  5. phytools

    A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes a diverse array of methods for visualiz...

  6. ActiveDriver

    A mutation analysis tool that discovers cancer driver genes with frequent mutations in protein signalling sites such as post-translational modifications (phosphorylation, ubiqui...

  7. PBSmapping

    This software has evolved from fisheries research conducted at the Pacific Biological Station (PBS) in 'Nanaimo', British Columbia, Canada. It extends the R language to include ...

  8. pathClass

    pathClass is a collection of classification methods that use information about feature connectivity in a biological network as an additional source of information. This addition...

  9. abd

    The abd package contains data sets and sample code for The Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009; Roberts & Company Publishers).

  10. FunCluster

    FunCluster performs a functional analysis of microarray expression data based on Gene Ontology & KEGG functional annotations. From expression data and functional annotations Fun...

  11. RLMM

    A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorith...

  12. SHIP

    The SHIP-package allows the estimation of various types of shrinkage covariance matrices. These types differ in terms of the so-called covariance target (to be chosen by the use...

  13. ddepn

    DDEPN (Dynamic Deterministic Effects Propagation Networks): Infer signalling networks for timecourse data. Given a matrix of high-throughput genomic or proteomic timecourse data...

  14. GFMaps

    GFMaps integrates datasets derived from gene expression profiles with preexisting information from public databases such as KEGG pathway or Gene Ontology using Gene Set Enrich...

  15. cellVolumeDist

    This package implements a methodology for using cell volume distributions to estimate cell growth rates and division times that is described in the paper entitled "Cell Volume D...

  16. clValid

    Statistical and biological validation of clustering results.

  17. FunNet

    FunNet is an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytic model implemented in this library involves two abstra...

  18. knorm

    This package provides Knorm correlations between genes (or probes) from microarray data obtained across multiple biologically interrelated experiments. The Knorm correlation ad...

  19. HDMD

    High Dimensional Molecular Data (HDMD) typically have many more variables or dimensions than observations or replicates (D>>N). This can cause many statistical procedures to fa...

  20. nparLD

    The package "nparLD" is designed to perform nonparametric analysis of longitudinal data in factorial experiments. Longitudinal data are those which are collected from the same s...

  21. sublogo

    Visualize correlation in biological sequence data using sublogo dendrogram plots.

  22. ArrayBin

    Fast adaptive binarization for numeric data arrays, particularly designed for high-throughput biological datasets. Includes options to filter out rows of the array with insuffic...

  23. kdetrees

    A non-parametric method for identifying potential outlying observations in a collection of phylogenetic trees based on the methods of Owen and Provan (2011). Such discordant tre...

  24. exsic

    The package provides tools for botanists, plant taxonomists, curators of plant genebanks and perhaps other biological collections.

  25. CLAG

    CLAG (for CLusters AGgregation) is an unsupervised non hierarchical clustering algorithm designed to cluster a large variety of biological data and to provide a clustered matrix...

  26. opmdata

    The package opm provides tools for analysing OmniLog(R) Phenotype Microarray (PM) data as produced by the device distributed by BIOLOG Inc. and similar kinds of data such as gro...

  27. mcpd

    The package provides some tools for botanists, taxonomists, curators of plant genebanks and perhaps other biological collections that make use of passport data for plant specime...

  28. PAGI

    The package can identify the dysregulated KEGG pathways based on global influence from the internal effect of pathways and crosstalk between pathways. (1) The PAGI package can p...

  29. sequences

    Educational package used in R courses to illustrate object-oriented programming and package development. Using biological sequences (DNA and RNA) as a working ...

  30. netClass

    netClass is an R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. This package adapts the following 5 algorit...

  31. lymphclon

    We provide a clonality score estimator that takes full advantage of the multi-biological-replicate structure of modern sequencing experiments; it specifically takes into account...

  32. ocean

    This package contains a set of functions for manipulating and visualizing output from numerical ocean models. Many of the routines are targeted towards Lagrangian particle-track...

  33. mlgt

    Processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample o...

  34. BVS

    The functions in this package focus on analyzing case-control association studies involving a group of genetic variants. In particular, we are interested in modeling the outcom...

  35. MultiChIPmixHMM

    Linear regression mixture model to ChIP-chip data analysis, taking into account the dependence (HMM), and for multiple biological samples.

  36. ccChooser

    ccChooser can be used to developing and evaluation of core collections for germplasm collections (entire collection). This package used to develop a core collection for biologic...

  37. MetaQC

    MetaQC implements our proposed quantitative quality control measures: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) exte...

  38. LGS

    The LGS package simulates the biological steps of a linkage group selection experiment in order to gain insights into the underlying biology. See Martinelli et al. (Proc Natl Ac...

  39. SynergizeR

    This package provides programmatic access to The Synergizer service for translating between sets of biological identifiers.

  40. ARTIVA

    Reversible Jump MCMC (RJ-MCMC)sampling for approximating the posterior distribution of a time varying regulatory network, under the Auto Regressive TIme VArying (ARTIVA) mode...

  41. pairheatmap

    A tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology.

  42. opm

    Tools for analysing OmniLog(R) and MicroStation(TM) phenotype microarray (PM) data as produced by the devices distributed by BIOLOG Inc. as well as similar kinds of data such as...

  43. bionetdata

    Data Package that includes several examples of chemical and biological data networks, i.e. data graph structured.

  44. selfea

    Functions using Cohen's effect sizes (Cohen, Jacob. Statistical power analysis for the behavioral sciences. Academic press, 2013) are provided for reliable feature selection in ...

  45. ESEA

    The package can identify the dysregulated canonical pathways by investigating the changes of biological relationships of pathways in the context of gene expression data. (1) The...

  46. SETPath

    Tests gene expression data from a biological pathway for biologically meaningful differences in the eigenstructure between two classes. Specifically, it tests the null hypothes...

  47. MetNorm

    Metabolomics data are inevitably subject to a component of unwanted variation, due to factors such as batch effects, matrix effects, and confounding biological variation. This p...

  48. monogeneaGM

    Geometric morphometric and evolutionary biology analyses of anchor shape from four-anchored monogeneans.

  49. pauwels2014

    Implementation of a Bayesian active learning strategy to carry out sequential experimental design in the context of biochemical network kinetic parameter estimation. This packag...

  50. BIOM.utils

    Provides utilities to facilitate import, export and computation with the BIOM (Biological Observation Matrix) format (http://biom-format.org).