Showing 42 of total 42 results (show query)
bioc
minfi:Analyze Illumina Infinium DNA methylation arrays
Tools to analyze & visualize Illumina Infinium methylation arrays.
Maintained by Kasper Daniel Hansen. Last updated 4 months ago.
immunooncologydnamethylationdifferentialmethylationepigeneticsmicroarraymethylationarraymultichanneltwochanneldataimportnormalizationpreprocessingqualitycontrol
60 stars 12.82 score 996 scripts 27 dependentsbioc
illuminaio:Parsing Illumina Microarray Output Files
Tools for parsing Illumina's microarray output files, including IDAT.
Maintained by Kasper Daniel Hansen. Last updated 5 months ago.
infrastructuredataimportmicroarrayproprietaryplatformsbioconductor
5 stars 10.28 score 58 scripts 37 dependentsbioc
methylumi:Handle Illumina methylation data
This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.
Maintained by Sean Davis. Last updated 5 months ago.
dnamethylationtwochannelpreprocessingqualitycontrolcpgisland
9 stars 9.90 score 89 scripts 9 dependents
statnet
statnet:Software Tools for the Statistical Analysis of Network Data
This package is designed to make it easy to install and load key packages from the 'statnet' suite in a single step. The `statnet` suite is a collection of packages for statistical network analysis that are designed to work together; they share common data representations, 'API' design and a uniform user interface. Together they provide an integrated set of tools for the exploration, visualization, statistical analysis, and simulation of many different forms of network data. Learn more about 'statnet' at <https://www.statnet.org>. Tutorials for many packages can be found at <https://github.com/statnet/Workshops/wiki>. For an introduction to functions in this package, type help(package='statnet').
Maintained by Martina Morris. Last updated 4 years ago.
41 stars 8.69 score 896 scriptsstatnet
ndtv:Network Dynamic Temporal Visualizations
Renders dynamic network data from 'networkDynamic' objects as movies, interactive animations, or other representations of changing relational structures and attributes.
Maintained by Skye Bender-deMoll. Last updated 9 months ago.
52 stars 8.30 score 254 scripts 1 dependentsbioc
netZooR:Unified methods for the inference and analysis of gene regulatory networks
netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.
Maintained by Tara Eicher. Last updated 14 days ago.
networkinferencenetworkgeneregulationgeneexpressiontranscriptionmicroarraygraphandnetworkgene-regulatory-networktranscription-factors
105 stars 7.98 scorebioc
beadarray:Quality assessment and low-level analysis for Illumina BeadArray data
The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
Maintained by Mark Dunning. Last updated 5 months ago.
microarrayonechannelqualitycontrolpreprocessing
7.88 score 70 scripts 4 dependentsbioc
wateRmelon:Illumina DNA methylation array normalization and metrics
15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.
Maintained by Leo C Schalkwyk. Last updated 4 months ago.
dnamethylationmicroarraytwochannelpreprocessingqualitycontrol
7.73 score 247 scripts 2 dependents
hrbrmstr
vegalite:Tools to Encode Visualizations with the 'Grammar of Graphics'-Like 'Vega-Lite' 'Spec'
The 'Vega-Lite' 'JavaScript' framework provides a higher-level grammar for visual analysis, akin to 'ggplot' or 'Tableau', that generates complete 'Vega' specifications. Functions exist which enable building a valid 'spec' from scratch or importing a previously created 'spec' file. Functions also exist to export 'spec' files and to generate code which will enable plots to be embedded in properly configured web pages. The default behavior is to generate an 'htmlwidget'.
Maintained by Bob Rudis. Last updated 7 years ago.
data-visualizationdatavisualizationvega-litevega-lite-specvisualizationwidget
158 stars 7.60 score 84 scriptsbioc
shinyMethyl:Interactive visualization for Illumina methylation arrays
Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.
Maintained by Jean-Philippe Fortin. Last updated 5 months ago.
dnamethylationmicroarraytwochannelpreprocessingqualitycontrolmethylationarray
5 stars 7.34 score 42 scriptsbioc
missMethyl:Analysing Illumina HumanMethylation BeadChip Data
Normalisation, testing for differential variability and differential methylation and gene set testing for data from Illumina's Infinium HumanMethylation arrays. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.
Maintained by Belinda Phipson. Last updated 29 days ago.
normalizationdnamethylationmethylationarraygenomicvariationgeneticvariabilitydifferentialmethylationgenesetenrichment
7.24 score 300 scripts 1 dependentsbioc
RnBeads:RnBeads
RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.
Maintained by Fabian Mueller. Last updated 2 months ago.
dnamethylationmethylationarraymethylseqepigeneticsqualitycontrolpreprocessingbatcheffectdifferentialmethylationsequencingcpgislandimmunooncologytwochanneldataimport
6.85 score 169 scripts 1 dependentsbioc
ChAMP:Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.
Maintained by Yuan Tian. Last updated 5 months ago.
microarraymethylationarraynormalizationtwochannelcopynumberdnamethylation
6.50 score 278 scriptsbioc
quantro:A test for when to use quantile normalization
A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.
Maintained by Stephanie Hicks. Last updated 5 months ago.
normalizationpreprocessingmultiplecomparisonmicroarraysequencing
6.40 score 69 scripts 2 dependentsbioc
recountmethylation:Access and analyze public DNA methylation array data compilations
Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.
Maintained by Sean K Maden. Last updated 5 months ago.
dnamethylationepigeneticsmicroarraymethylationarrayexperimenthub
9 stars 6.28 score 9 scriptsbioc
lumi:BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.
Maintained by Lei Huang. Last updated 5 months ago.
microarrayonechannelpreprocessingdnamethylationqualitycontroltwochannel
6.26 score 294 scripts 5 dependentsbioc
iNETgrate:Integrates DNA methylation data with gene expression in a single gene network
The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes.
Maintained by Habil Zare. Last updated 5 months ago.
geneexpressionrnaseqdnamethylationnetworkinferencenetworkgraphandnetworkbiomedicalinformaticssystemsbiologytranscriptomicsclassificationclusteringdimensionreductionprincipalcomponentmrnamicroarraynormalizationgenepredictionkeggsurvivalcore-services
74 stars 6.21 score 1 scriptsbioc
ENmix:Quality control and analysis tools for Illumina DNA methylation BeadChip
Tools for quanlity control, analysis and visulization of Illumina DNA methylation array data.
Maintained by Zongli Xu. Last updated 18 days ago.
dnamethylationpreprocessingqualitycontroltwochannelmicroarrayonechannelmethylationarraybatcheffectnormalizationdataimportregressionprincipalcomponentepigeneticsmultichanneldifferentialmethylationimmunooncology
6.01 score 115 scriptsbioc
arrayQualityMetrics:Quality metrics report for microarray data sets
This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.
Maintained by Mike Smith. Last updated 5 months ago.
microarrayqualitycontrolonechanneltwochannelreportwriting
1 stars 5.98 score 193 scriptsbioc
REMP:Repetitive Element Methylation Prediction
Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE.
Maintained by Yinan Zheng. Last updated 5 months ago.
dnamethylationmicroarraymethylationarraysequencinggenomewideassociationepigeneticspreprocessingmultichanneltwochanneldifferentialmethylationqualitycontroldataimport
2 stars 5.94 score 18 scriptsbioc
deconvR:Simulation and Deconvolution of Omic Profiles
This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.
Maintained by Irem B. Gündüz. Last updated 5 months ago.
dnamethylationregressiongeneexpressionrnaseqsinglecellstatisticalmethodtranscriptomicsbioconductor-packagedeconvolutiondna-methylationomics
10 stars 5.78 score 15 scriptsbioc
methylclock:Methylclock - DNA methylation-based clocks
This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.
Maintained by Dolors Pelegri-Siso. Last updated 5 months ago.
dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationcpp
39 stars 5.52 score 28 scriptsbioc
conumee:Enhanced copy-number variation analysis using Illumina DNA methylation arrays
This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays.
Maintained by Volker Hovestadt. Last updated 5 months ago.
copynumbervariationdnamethylationmethylationarraymicroarraynormalizationpreprocessingqualitycontrolsoftware
5.48 score 30 scriptsbioc
bigmelon:Illumina methylation array analysis for large experiments
Methods for working with Illumina arrays using gdsfmt.
Maintained by Leonard C. Schalkwyk. Last updated 5 months ago.
dnamethylationmicroarraytwochannelpreprocessingqualitycontrolmethylationarraydataimportcpgisland
5.47 score 21 scriptsbioc
VanillaICE:A Hidden Markov Model for high throughput genotyping arrays
Hidden Markov Models for characterizing chromosomal alteration in high throughput SNP arrays.
Maintained by Robert Scharpf. Last updated 5 months ago.
5.36 score 63 scripts 1 dependentsbioc
methylCC:Estimate the cell composition of whole blood in DNA methylation samples
A tool to estimate the cell composition of DNA methylation whole blood sample measured on any platform technology (microarray and sequencing).
Maintained by Stephanie C. Hicks. Last updated 5 months ago.
microarraysequencingdnamethylationmethylationarraymethylseqwholegenome
19 stars 5.18 score 8 scriptsbioc
shinyepico:ShinyÉPICo
ShinyÉPICo is a graphical pipeline to analyze Illumina DNA methylation arrays (450k or EPIC). It allows to calculate differentially methylated positions and differentially methylated regions in a user-friendly interface. Moreover, it includes several options to export the results and obtain files to perform downstream analysis.
Maintained by Octavio Morante-Palacios. Last updated 5 months ago.
differentialmethylationdnamethylationmicroarraypreprocessingqualitycontrol
5 stars 5.00 score 1 scriptsbioc
crlmm:Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.
Maintained by Benilton S Carvalho. Last updated 28 days ago.
microarraypreprocessingsnpcopynumbervariation
4.78 score 37 scripts 3 dependentsbioc
MethylAid:Visual and interactive quality control of large Illumina DNA Methylation array data sets
A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.
Maintained by L.J.Sinke. Last updated 5 months ago.
dnamethylationmethylationarraymicroarraytwochannelqualitycontrolbatcheffectvisualizationgui
4.51 score 16 scriptsbioc
yarn:YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.
Maintained by Joseph N Paulson. Last updated 5 months ago.
softwarequalitycontrolgeneexpressionsequencingpreprocessingnormalizationannotationvisualizationclustering
4.49 score 31 scriptsbioc
MAGAR:MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.
Maintained by Michael Scherer. Last updated 5 months ago.
regressionepigeneticsdnamethylationsnpgeneticvariabilitymethylationarraymicroarraycpgislandmethylseqsequencingmrnamicroarraypreprocessingcopynumbervariationtwochannelimmunooncologydifferentialmethylationbatcheffectqualitycontroldataimportnetworkclusteringgraphandnetwork
4.30 score 3 scriptsbioc
epimutacions:Robust outlier identification for DNA methylation data
The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.
Maintained by Dolors Pelegri-Siso. Last updated 5 months ago.
dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationcpp
4.23 score 28 scripts
r-forge
RobLoxBioC:Infinitesimally Robust Estimators for Preprocessing -Omics Data
Functions for the determination of optimally robust influence curves and estimators for preprocessing omics data, in particular gene expression data (Kohl and Deigner (2010), <doi:10.1186/1471-2105-11-583>).
Maintained by Matthias Kohl. Last updated 2 months ago.
4.03 score 30 scriptsbioc
funtooNorm:Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
Provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.
Maintained by Kathleen Klein. Last updated 5 months ago.
dnamethylationpreprocessingnormalization
3.70 scorebioc
MinimumDistance:A Package for De Novo CNV Detection in Case-Parent Trios
Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.
Maintained by Robert Scharpf. Last updated 5 months ago.
microarraysnpcopynumbervariation
3.60 score 10 scriptsbioc
epigenomix:Epigenetic and gene transcription data normalization and integration with mixture models
A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.
Maintained by Hans-Ulrich Klein. Last updated 5 months ago.
chipseqgeneexpressiondifferentialexpressionclassification
3.30 score 1 scriptsbioc
normalize450K:Preprocessing of Illumina Infinium 450K data
Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.
Maintained by Jonathan Alexander Heiss. Last updated 5 months ago.
normalizationdnamethylationmicroarraytwochannelpreprocessingmethylationarray
3.30 score 1 scriptsbioc
blima:Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level
Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.
Maintained by Vojtěch Kulvait. Last updated 5 months ago.
microarraypreprocessingnormalizationdifferentialexpressiongeneregulationgeneexpressioncpp
3.30 score 1 scriptsbioc
ffpe:Quality assessment and control for FFPE microarray expression data
Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).
Maintained by Levi Waldron. Last updated 5 months ago.
microarraygeneexpressionqualitycontrol
3.03 score 27 scriptsbioc
iCheck:QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.
Maintained by Weiliang Qiu. Last updated 5 months ago.
geneexpressiondifferentialexpressionmicroarraypreprocessingdnamethylationonechanneltwochannelqualitycontrol
3.00 score 1 scripts
wolfgangrolke
moodlequizR:Easily Create Fully Randomized 'Moodle' Test Questions
Routines to generate fully randomized 'moodle' quizzes. It also contains 15 examples and a 'shiny' app.
Maintained by Wolfgang Rolke. Last updated 10 months ago.
2.30 score 1 scripts
nie-xiuquan
EMAS:Epigenome-Wide Mediation Analysis Study
DNA methylation is essential for human, and environment can change the DNA methylation and affect body status. Epigenome-Wide Mediation Analysis Study (EMAS) can find potential mediator CpG sites between exposure (x) and outcome (y) in epigenome-wide. For more information on the methods we used, please see the following references: Tingley, D. (2014) <doi:10.18637/jss.v059.i05>, Turner, S. D. (2018) <doi:10.21105/joss.00731>, Rosseel, D. (2012) <doi:10.18637/jss.v048.i02>.
Maintained by Xiuquan Nie. Last updated 3 years ago.
1.00 score