Showing 8 of total 8 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
aroma.light:Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.
Maintained by Henrik Bengtsson. Last updated 5 months ago.
infrastructuremicroarrayonechanneltwochannelmultichannelvisualizationpreprocessingbioconductor
1 stars 6.43 score 26 scripts 20 dependentsbioc
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
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
cytoviewer:An interactive multi-channel image viewer for R
This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization and supports image downloads.
Maintained by Lasse Meyer. Last updated 5 months ago.
immunooncologysoftwaresinglecellonechanneltwochannelmultichannelspatialdataimportbioconductorimagingshinyvisualization
7 stars 5.50 score 15 scriptsbioc
Polytect:An R package for digital data clustering
Polytect is an advanced computational tool designed for the analysis of multi-color digital PCR data. It provides automatic clustering and labeling of partitions into distinct groups based on clusters first identified by the flowPeaks algorithm. Polytect is particularly useful for researchers in molecular biology and bioinformatics, enabling them to gain deeper insights into their experimental results through precise partition classification and data visualization.
Maintained by Yao Chen. Last updated 3 months ago.
ddpcrclusteringmultichannelclassification
4.74 score 4 scriptsbioc
snm:Supervised Normalization of Microarrays
SNM is a modeling strategy especially designed for normalizing high-throughput genomic data. The underlying premise of our approach is that your data is a function of what we refer to as study-specific variables. These variables are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.
Maintained by John D. Storey. Last updated 5 months ago.
microarrayonechanneltwochannelmultichanneldifferentialexpressionexonarraygeneexpressiontranscriptionmultiplecomparisonpreprocessingqualitycontrol
4.41 score 64 scripts
henrikbengtsson
aroma.core:Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
Maintained by Henrik Bengtsson. Last updated 2 years ago.
microarrayonechanneltwochannelmultichanneldataimportdatarepresentationguivisualizationpreprocessingqualitycontrolacghcopynumbervariants
1 stars 4.30 score 16 scripts 6 dependents