Tools   Select Another Resource Report Type

http://www.bioconductor.org/packages/release/bioc/html/PAPi.html

An R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation.

Proper citation: PAPi (RRID:SCR_002857) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/CNVassoc/

Software package that carries out association analysis of common copy number variants in population-based studies. It includes functions for analysing association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. It also includes functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis.

Proper citation: CNVassoc (RRID:SCR_002901) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/tweeDEseq.html

Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.

Proper citation: tweeDEseq (RRID:SCR_003038) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/R-pbh5

Software library for accessing data in HDF5 files produced by Pacific Biosciences sequencing machines. The R package supports accessing data from: cmp.h5, bas.h5, pls.h5, and trc.h5.

Proper citation: R-pbh5 (RRID:SCR_003026) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/isopat/

Software function that calculates the isotopic pattern (fine structures) for a given chemical formula.

Proper citation: Isopat (RRID:SCR_003025) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/BRAIN.html

Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S).

Proper citation: BRAIN (RRID:SCR_003018) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/survcomp.html

R package providing functions to assess and to compare the performance of risk prediction (survival) models.

Proper citation: SurvComp (RRID:SCR_003054) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/ptw/

Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation).

Proper citation: Parametric Time Warping (RRID:SCR_003053) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/R-pbutils

An R software package providing plotting and convenience functions.

Proper citation: R-pbutils (RRID:SCR_002995) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/edgeR/

Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.

Proper citation: edgeR (RRID:SCR_012802) Copy   

•   Source: SciCrunch Registry

http://www.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software program that performs estimation of power and sample sizes required to detect genetic and environmental main, as well as gene-environment interaction (GxE) effects in indirect matched case-control studies (1:1 matching). When the hypothesis of GxE is tested, power/sample size will be estimated for the detection of GxE, as well as for the detection of genetic and environmental marginal effects. Furthermore, power estimation is implemented for the joint test of genetic marginal and GxE effects (Kraft P et al., 2007). Power and sample size estimations are based on Gauderman''s (2002) asymptotic approach for power and sample size estimations in direct studies of GxE. Hardy-Weinberg equilibrium and independence of genotypes and environmental exposures in the population are assumed. The estimates are based on genotypic codes (G=1 (G=0) for individuals who carry a (non-) risk genotype), which depend on the mode of inheritance (dominant, recessive, or multiplicative). A conditional logistic regression approach is used, which employs a likelihood-ratio test with respect to a biallelic candidate SNP, a binary environmental factor (E=1 (E=0) in (un)exposed individuals), and the interaction between these components. (entry from Genetic Analysis Software)

Proper citation: PIAGE (RRID:SCR_013124) Copy   

•   Source: SciCrunch Registry

http://folk.uio.no/thoree/FEST/

An R package for simulations and likelihood calculations of pair-wise family relationships using DNA marker data. (entry from Genetic Analysis Software)

Proper citation: R/FEST (RRID:SCR_013347) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/HMP/index.html

An R-package which uses Dirichlet-Multinomial distribution to perform formal hypothesis testing on the species abundance distribution of human microbiome data, and to calculate power and sample size requirements for human microbiome experiments.

Proper citation: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP (RRID:SCR_014612) Copy   

•   Source: SciCrunch Registry

http://stat.ethz.ch/R-manual/R-patched/library/stats/html/hclust.html

R documentation for hierarchical cluster analysis on a set of dissimilarities for n objects. Each object is assigned to its own cluster, which an algorithm proceeds through iteratively. Two of the most similar clusters are joined at each stage until there is a single cluster. Distances between clusters are recomputed at each stage by the Lance–Williams dissimilarity update formula according to the particular clustering method being used. Clustering methods include: Ward's minimum variance method, complete linkage method, and single linkage method.

Proper citation: Hierarchical Clustering (RRID:SCR_014673) Copy   

•   Source: SciCrunch Registry

https://github.com/jakejh/zeitzeiger

R package for regularized supervised learning on high-dimensional data from an oscillatory system. Zeitzeiger can quantify rhythmic behavior, make accurate predictions, identify major patterns and important features, and detect when the oscillator is perturbed.

Proper citation: Zeitzeiger (RRID:SCR_014791) Copy   

•   Source: SciCrunch Registry

http://stat.ethz.ch/R-manual/R-patched/library/stats/html/prcomp.html

R documentation for a function that performs a principal components analysis on a given data matrix and returns the results as an object of class prcomp.

Proper citation: Principal Components Analysis (RRID:SCR_014676) Copy   

•   Source: SciCrunch Registry

http://stat.ethz.ch/R-manual/R-devel/library/MASS/html/lda.html

R documentation for a function to perform linear discriminant analysis; specifically, to detect if the within-class covariance matrix is singular.

Proper citation: Linear Discriminant Analysis (RRID:SCR_014675) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=NBR

Software tool as implementation of network based statistics toolbox in R. Includes mixed effects models.

Proper citation: Network-Based R-Statistics (RRID:SCR_019114) Copy   

•   Source: SciCrunch Registry

http://artiva.gene-networks.net/artiva-2/

Algorithm available in a R package that is a statistical framework to infer time-varying structures of gene-regulation networks.

Proper citation: ARTIVA (RRID:SCR_011946) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/adtex/

A software tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples.

Proper citation: ADTEx (RRID:SCR_012059) Copy   

•   Source: SciCrunch Registry