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r-ecodist
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public |
Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community data.
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2025-04-22 |
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r-adephylo
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public |
Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.
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2025-04-22 |
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r-phylobase
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public |
Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
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2025-04-22 |
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r-rnexml
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public |
Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
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2025-04-22 |
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bioconductor-flowsorted.blood.450k
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public |
Illumina HumanMethylation data on sorted blood cell populations
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2025-04-22 |
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bioconductor-pathprint
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public |
Pathway fingerprinting for analysis of gene expression arrays
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2025-04-22 |
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r-sbpiper
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public |
Provides an API for analysing repetitive parameter estimations and simulations of mathematical models. Examples of mathematical models are Ordinary Differential equations (ODEs) or Stochastic Differential Equations (SDEs) models. Among the analyses for parameter estimation 'sbpiper' calculates statistics and generates plots for parameter density, PCA of the best fits, parameter profile likelihood estimations (PLEs), and 2D parameter PLEs. These results can be generated using all or a subset of the best computed parameter sets. Among the analyses for model simulation 'sbpiper' calculates statistics and generates plots for deterministic and stochastic time courses via cartesian and heatmap plots. Plots for the scan of one or two model parameters can also be generated. This package is primarily used by the software 'SBpipe'. Citation: Dalle Pezze P, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology. 2017;11:46. <doi:10.1186/s12918-017-0423-3>.
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2025-04-22 |
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r-rapidr
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public |
Package to perform non-invasive fetal testing for aneuploidies using sequencing count data from cell-free DNA
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2025-04-22 |
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bioconductor-mspuritydata
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public |
Fragmentation spectral libraries and data to test the msPurity package
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2025-04-22 |
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r-seqminer
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public |
Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
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2025-04-22 |
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r-shazam
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public |
Provides a computational framework for analyzing mutations in immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection pressure, mutational load quantification, building of somatic hypermutation (SHM) models, and model-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>, Yaari, et al (2012) <doi:10.1093/nar/gks457>, Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>, Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
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2025-04-22 |
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r-sigqc
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public |
Provides gene signature quality control metrics in publication ready plots. Namely, enables the visualization of properties such as expression, variability, correlation, and comparison of methods of standardisation and scoring metrics.
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2025-04-22 |
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r-fmsb
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public |
Several utility functions for the book entitled "Practices of Medical and Health Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.
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2025-04-22 |
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bioconductor-interest
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public |
Intron-Exon Retention Estimator
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2025-04-22 |
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r-stampp
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public |
Allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. <doi
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2025-04-22 |
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r-pegas
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public |
Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
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2025-04-22 |
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bioconductor-snprelate
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public |
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
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2025-04-22 |
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bioconductor-gdsfmt
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public |
R Interface to CoreArray Genomic Data Structure (GDS) Files
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2025-04-22 |
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bioconductor-biocfilecache
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public |
Manage Files Across Sessions
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2025-04-22 |
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bioconductor-consensusov
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public |
Gene expression-based subtype classification for high-grade serous ovarian cancer
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2025-04-22 |
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bioconductor-zfpkm
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public |
A suite of functions to facilitate zFPKM transformations
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2025-04-22 |
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bioconductor-interminer
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public |
R Interface with InterMine-Powered Databases
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2025-04-22 |
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bioconductor-apeglm
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public |
Approximate posterior estimation for GLM coefficients
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2025-04-22 |
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bioconductor-nadfinder
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public |
Call wide peaks for sequencing data
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2025-04-22 |
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bioconductor-maftools
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public |
Summarize, Analyze and Visualize MAF Files
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2025-04-22 |
