|
bioconductor-props
|
public |
PRObabilistic Pathway Score (PROPS)
|
2025-03-25 |
|
bioconductor-minfidataepic
|
public |
Example data for the Illumina Methylation EPIC array
|
2025-03-25 |
|
bioconductor-minfidata
|
public |
Example data for the Illumina Methylation 450k array
|
2025-03-25 |
|
bioconductor-methyvimdata
|
public |
Example experimental data for use with the methyvim package
|
2025-03-25 |
|
bioconductor-methyvim
|
public |
Targeted, Robust, and Model-free Differential Methylation Analysis
|
2025-03-25 |
|
bioconductor-methylaiddata
|
public |
MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples
|
2025-03-25 |
|
bioconductor-methylaid
|
public |
Visual and interactive quality control of large Illumina DNA Methylation array data sets
|
2025-03-25 |
|
bioconductor-flowsorted.blood.epic
|
public |
Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells
|
2025-03-25 |
|
bioconductor-funtoonorm
|
public |
Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
|
2025-03-25 |
|
bioconductor-illuminahumanmethylation27kmanifest
|
public |
Manifest for Illumina's 27k array data
|
2025-03-25 |
|
bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19
|
public |
An annotation package for Illumina's EPIC methylation arrays.
|
2025-03-25 |
|
bioconductor-flowsorted.dlpfc.450k
|
public |
Illumina HumanMethylation data on sorted frontal cortex cell populations
|
2025-03-25 |
|
bioconductor-flowsorted.cordbloodnorway.450k
|
public |
Illumina HumanMethylation data on sorted cord blood cell populations
|
2025-03-25 |
|
bioconductor-flowsorted.cordblood.450k
|
public |
Illumina 450k data on sorted cord blood cells
|
2025-03-25 |
|
bioconductor-hmyrib36
|
public |
YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes
|
2025-03-25 |
|
bioconductor-ceuhm3
|
public |
ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort
|
2025-03-25 |
|
bioconductor-ceu1kg
|
public |
CEU (N=60) genotypes from 1000 genomes pilot phase I
|
2025-03-25 |
|
bioconductor-compartmap
|
public |
Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seq
|
2025-03-25 |
|
bioconductor-yri1kgv
|
public |
expression + genotype on 79 unrelated YRI individuals
|
2025-03-25 |
|
bioconductor-ggdata
|
public |
all 90 hapmap CEU samples, 47K expression, 4mm SNP
|
2025-03-25 |
|
bioconductor-yrimulti
|
public |
support for expression, methylation, DHS, VCF for YRI
|
2025-03-25 |
|
bioconductor-dsqtl
|
public |
dsQTL, data excerpt from Degner et al. 2012 Nature letter
|
2025-03-25 |
|
bioconductor-ceu1kgv
|
public |
expression + genotype on 79 unrelated CEU individuals
|
2025-03-25 |
|
bioconductor-clipper
|
public |
Gene Set Analysis Exploiting Pathway Topology
|
2025-03-25 |
|
bioconductor-geneanswers
|
public |
Integrated Interpretation of Genes
|
2025-03-25 |
|
bioconductor-pigengene
|
public |
Infers biological signatures from gene expression data
|
2025-03-25 |
|
bioconductor-mcbiclust
|
public |
Massive correlating biclusters for gene expression data and associated methods
|
2025-03-25 |
|
bioconductor-fastliquidassociation
|
public |
functions for genome-wide application of Liquid Association
|
2025-03-25 |
|
bioconductor-randomwalkrestartmh
|
public |
Random walk with restart on multiplex and heterogeneous Networks
|
2025-03-25 |
|
r-dnet
|
public |
The focus of the dnet by Fang and Gough (2014) <doi:10.1186/s13073-014-0064-8> is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including: human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.
|
2025-03-25 |
|
bioconductor-appreci8r
|
public |
appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV
|
2025-03-25 |
|
r-rsnps
|
public |
A programmatic interface to various 'SNP' 'datasets' on the web: 'OpenSNP' (<https://opensnp.org>), and 'NBCIs' 'dbSNP' database (<https://www.ncbi.nlm.nih.gov/projects/SNP>). Functions are included for searching for 'NCBI'. For 'OpenSNP', functions are included for getting 'SNPs', and data for 'genotypes', 'phenotypes', annotations, and bulk downloads of data by user.
|
2025-03-25 |
|
bioconductor-metnet
|
public |
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
|
2025-03-25 |
|
bioconductor-zebrafishprobe
|
public |
This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Zebrafish\_probe\_tab.
|
2025-03-25 |
|
bioconductor-zebrafishcdf
|
public |
A package containing an environment representing the Zebrafish.cdf file.
|
2025-03-25 |
|
bioconductor-zebrafish.db0
|
public |
Base Level Annotation databases for zebrafish
|
2025-03-25 |
|
bioconductor-zebrafish.db
|
public |
Affymetrix Affymetrix Zebrafish Array annotation data (chip zebrafish)
|
2025-03-25 |
|
bioconductor-ygs98probe
|
public |
This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was YG-S98\_probe\_tab.
|
2025-03-25 |
|
bioconductor-ygs98cdf
|
public |
A package containing an environment representing the YG_S98.cdf file.
|
2025-03-25 |
|
bioconductor-ygs98.db
|
public |
Affymetrix Affymetrix YG_S98 Array annotation data (chip ygs98)
|
2025-03-25 |
|
bioconductor-yeast2probe
|
public |
This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Yeast\_2\_probe\_tab.
|
2025-03-25 |
|
bioconductor-yeast2cdf
|
public |
A package containing an environment representing the Yeast_2.cdf file.
|
2025-03-25 |
|
bioconductor-yeast2.db
|
public |
Affymetrix Affymetrix Yeast_2 Array annotation data (chip yeast2)
|
2025-03-25 |
|
bioconductor-yeast.db0
|
public |
Base Level Annotation databases for yeast
|
2025-03-25 |
|
bioconductor-ye6100subdcdf
|
public |
A package containing an environment representing the Ye6100subD.CDF file.
|
2025-03-25 |
|
bioconductor-ye6100subccdf
|
public |
A package containing an environment representing the Ye6100subC.CDF file.
|
2025-03-25 |
|
bioconductor-ye6100subbcdf
|
public |
A package containing an environment representing the Ye6100subB.CDF file.
|
2025-03-25 |
|
r-hardyweinberg
|
public |
Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) <doi:10.1126/science.28.706.49> for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi: 10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
|
2025-03-25 |
|
bioconductor-ye6100subacdf
|
public |
A package containing an environment representing the Ye6100subA.CDF file.
|
2025-03-25 |
|
bioconductor-xtropicalisprobe
|
public |
This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was X\_tropicalis\_probe\_tab.
|
2025-03-25 |
