Bioconductor Topics

Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.

Analyze and correct probe positional bias in microarray data due to RNA degradation

Processing and Differential Expression Analysis of Agilent microRNA chips

Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

Chromosmal Aberrations Finder in Expression data

Create Copy-Number Plots using karyoploteR functionality

Methylation array and sequencing spatial analysis methods

Ensemble of Gene Set Enrichment Analyses

Quality control and analysis tools for Illumina DNA methylation BeadChip

Expression Weighted Celltype Enrichment

R functions for the normalization of Exiqon miRNA array data

Get data from NCBI Gene Expression Omnibus (GEO)

GeneRegionScan

Global test for groups of variables via model comparisons

Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Statistical Characterization of Post-translational Modifications

MSstats GUI for Statistical Anaylsis of Proteomics Experiments

PAA (Protein Array Analyzer)

Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)

PRojection Onto the Most Interesting Statistical Evidence

A Genotype Calling Algorithm for Affymetrix SNP Arrays

Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)

Signal-to-Noise applied to Gene Expression Experiments

A fast scatterplot smoother suitable for microarray normalization

Affymetrix File Parsing SDK

Methods for Affymetrix Oligonucleotide Arrays

Linear Model of background subtraction and the Langmuir isotherm

Methods for fitting probe-level models

Graphics Toolbox for Assessment of Affymetrix Expression Measures

Functions useful for those doing repetitive analyses with Affymetrix GeneChips

GUI for limma Package with Affymetrix Microarrays

alternative CDF environments (aka probeset mappings)

Annotation tools for Affymetrix biological metadata

Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

Quality metrics report for microarray data sets

Quality assessment and low-level analysis for Illumina BeadArray data

A package for the clinical proteomic profiling data analysis

Manipulation of Codelink microarray data

Functions to perform cancer outlier profile analysis.

Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

Differential expression using kernel-based score test

Visualization of highly multiplexed imaging data in R

An interactive multi-channel image viewer for R

Differential Co-expression Analysis

GaGa hierarchical model for high-throughput data analysis

Generally Applicable Gene-set Enrichment for Pathway Analysis

Background Adjustment Using Sequence Information

Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing