R-universe search: topic:onechannel

bioc

limma:Linear Models for Microarray and Omics Data

Data analysis, linear models and differential expression for omics data.

Maintained by Gordon Smyth. Last updated 11 days ago.

exonarray geneexpression transcription alternativesplicing differentialexpression differentialsplicing genesetenrichment dataimport bayesian clustering regression timecourse microarray micrornaarray mrnamicroarray onechannel proprietaryplatforms twochannel sequencing rnaseq batcheffect multiplecomparison normalization preprocessing qualitycontrol biomedicalinformatics cellbiology cheminformatics epigenetics functionalgenomics genetics immunooncology metabolomics proteomics systemsbiology transcriptomics

13.81 score 16k scripts 586 dependents

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GEOquery:Get data from NCBI Gene Expression Omnibus (GEO)

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.

Maintained by Sean Davis. Last updated 5 months ago.

microarray dataimport onechannel twochannel sage bioconductor bioinformatics data-science genomics ncbi-geo

93 stars 13.48 score 4.1k scripts 45 dependents

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karyoploteR:Plot customizable linear genomes displaying arbitrary data

karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

Maintained by Bernat Gel. Last updated 5 months ago.

visualization copynumbervariation sequencing coverage dnaseq chipseq methylseq dataimport onechannel bioconductor bioinformatics data-visualization genome genomics-visualization plotting-in-r

307 stars 11.25 score 656 scripts 4 dependents

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affy:Methods for Affymetrix Oligonucleotide Arrays

The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.

Maintained by Robert D. Shear. Last updated 3 months ago.

microarray onechannel preprocessing

11.12 score 2.5k scripts 98 dependents

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oligo:Preprocessing tools for oligonucleotide arrays

A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

Maintained by Benilton Carvalho. Last updated 21 days ago.

microarray onechannel twochannel preprocessing snp differentialexpression exonarray geneexpression dataimport zlib

3 stars 10.42 score 528 scripts 10 dependents

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cytomapper:Visualization of highly multiplexed imaging data in R

Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells.

Maintained by Lasse Meyer. Last updated 5 months ago.

immunooncology software singlecell onechannel twochannel multiplecomparison normalization dataimport bioimaging imaging-mass-cytometry single-cell spatial-analysis

32 stars 9.61 score 354 scripts 5 dependents

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EWCE:Expression Weighted Celltype Enrichment

Used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.

Maintained by Alan Murphy. Last updated 1 months ago.

geneexpression transcription differentialexpression genesetenrichment genetics microarray mrnamicroarray onechannel rnaseq biomedicalinformatics proteomics visualization functionalgenomics singlecell deconvolution single-cell single-cell-rna-seq transcriptomics

56 stars 9.29 score 99 scripts

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gage:Generally Applicable Gene-set Enrichment for Pathway Analysis

GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.

Maintained by Weijun Luo. Last updated 5 months ago.

pathways go differentialexpression microarray onechannel twochannel rnaseq genetics multiplecomparison genesetenrichment geneexpression systemsbiology sequencing

5 stars 8.68 score 784 scripts 1 dependents

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vsn:Variance stabilization and calibration for microarray data

The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

Maintained by Wolfgang Huber. Last updated 5 months ago.

microarray onechannel twochannel preprocessing

8.49 score 924 scripts 51 dependents

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affxparser:Affymetrix File Parsing SDK

Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

Maintained by Kasper Daniel Hansen. Last updated 3 months ago.

infrastructure dataimport microarray proprietaryplatforms onechannel bioconductor cpp

7 stars 8.19 score 65 scripts 14 dependents

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MSstatsPTM:Statistical Characterization of Post-translational Modifications

MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.

Maintained by Devon Kohler. Last updated 4 months ago.

immunooncology massspectrometry proteomics software differentialexpression onechannel twochannel normalization qualitycontrol post-translational-modification cpp

10 stars 8.03 score 36 scripts 2 dependents

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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.

microarray onechannel qualitycontrol preprocessing

7.88 score 70 scripts 4 dependents

henrikbengtsson

PSCBS:Analysis of Parent-Specific DNA Copy Numbers

Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

acgh copynumbervariants snp microarray onechannel twochannel genetics

7 stars 7.63 score 34 scripts 9 dependents

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gcrma:Background Adjustment Using Sequence Information

Background adjustment using sequence information

Maintained by Z. Wu. Last updated 5 months ago.

microarray onechannel preprocessing

7.28 score 164 scripts 11 dependents

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affyPLM:Methods for fitting probe-level models

A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.

Maintained by Ben Bolstad. Last updated 2 months ago.

microarray onechannel preprocessing qualitycontrol openblas zlib

6.99 score 206 scripts 4 dependents

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diffcoexp:Differential Co-expression Analysis

A tool for the identification of differentially coexpressed links (DCLs) and differentially coexpressed genes (DCGs). DCLs are gene pairs with significantly different correlation coefficients under two conditions. DCGs are genes with significantly more DCLs than by chance.

Maintained by Wenbin Wei. Last updated 5 months ago.

geneexpression differentialexpression transcription microarray onechannel twochannel rnaseq sequencing coverage immunooncology

15 stars 6.89 score 37 scripts

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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.

infrastructure microarray onechannel twochannel multichannel visualization preprocessing bioconductor

1 stars 6.43 score 26 scripts 20 dependents

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MSstatsShiny:MSstats GUI for Statistical Anaylsis of Proteomics Experiments

MSstatsShiny is an R-Shiny graphical user interface (GUI) integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM. It provides a point and click end-to-end analysis pipeline applicable to a wide variety of experimental designs. These include data-dependedent acquisitions (DDA) which are label-free or tandem mass tag (TMT)-based, as well as DIA, SRM, and PRM acquisitions and those targeting post-translational modifications (PTMs). The application automatically saves users selections and builds an R script that recreates their analysis, supporting reproducible data analysis.

Maintained by Devon Kohler. Last updated 5 months ago.

immunooncology massspectrometry proteomics software shinyapps differentialexpression onechannel twochannel normalization qualitycontrol gui

15 stars 6.31 score 4 scripts

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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.

microarray onechannel preprocessing dnamethylation qualitycontrol twochannel

6.26 score 294 scripts 5 dependents

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CopyNumberPlots:Create Copy-Number Plots using karyoploteR functionality

CopyNumberPlots have a set of functions extending karyoploteRs functionality to create beautiful, customizable and flexible plots of copy-number related data.

Maintained by Bernat Gel. Last updated 5 months ago.

visualization copynumbervariation coverage onechannel dataimport sequencing dnaseq bioconductor bioconductor-package bioinformatics copy-number-variation genomics genomics-visualization

6 stars 6.24 score 16 scripts 2 dependents

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affycoretools:Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.

Maintained by James W. MacDonald. Last updated 5 months ago.

reportwriting microarray onechannel geneexpression

6.07 score 117 scripts

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

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

Maintained by Jose Marugan. Last updated 22 days ago.

microarray dataimport onechannel twochannel

6.05 score 124 scripts 1 dependents

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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 15 days ago.

dnamethylation preprocessing qualitycontrol twochannel microarray onechannel methylationarray batcheffect normalization dataimport regression principalcomponent epigenetics multichannel differentialmethylation immunooncology

6.01 score 115 scripts

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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.

microarray qualitycontrol onechannel twochannel reportwriting

1 stars 5.98 score 193 scripts

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affycomp:Graphics Toolbox for Assessment of Affymetrix Expression Measures

The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.

Maintained by Robert D. Shear. Last updated 5 months ago.

onechannel microarray preprocessing

5.92 score 14 scripts

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

The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

Maintained by Jelle Goeman. Last updated 5 months ago.

microarray onechannel bioinformatics differentialexpression go pathways

5.89 score 79 scripts 6 dependents

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makecdfenv:CDF Environment Maker

This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.

Maintained by James W. MacDonald. Last updated 3 months ago.

onechannel dataimport preprocessing zlib

5.81 score 36 scripts 2 dependents

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EGSEA:Ensemble of Gene Set Enrichment Analyses

This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. EGSEA algorithm utilizes the analysis results of twelve prominent GSE algorithms in the literature to calculate collective significance scores for each gene set.

Maintained by Monther Alhamdoosh. Last updated 5 months ago.

immunooncology differentialexpression go geneexpression genesetenrichment genetics microarray multiplecomparison onechannel pathways rnaseq sequencing software systemsbiology twochannel metabolomics proteomics kegg graphandnetwork genesignaling genetarget networkenrichment network classification

5.81 score 64 scripts

henrikbengtsson

aroma.affymetrix:Analysis of Large Affymetrix Microarray Data Sets

A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

infrastructure proprietaryplatforms exonarray microarray onechannel gui dataimport datarepresentation preprocessing qualitycontrol visualization reportwriting acgh copynumbervariants differentialexpression geneexpression snp transcription affymetrix analysis copy-number dna expression hpc large-scale notebook reproducibility rna

10 stars 5.79 score 112 scripts 3 dependents

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annaffy:Annotation tools for Affymetrix biological metadata

Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.

Maintained by Colin A. Smith. Last updated 5 months ago.

onechannel microarray annotation go pathways reportwriting

5.64 score 60 scripts 3 dependents

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MSstatsLiP:LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

Maintained by Devon Kohler. Last updated 5 months ago.

immunooncology massspectrometry proteomics software differentialexpression onechannel twochannel normalization qualitycontrol cpp

7 stars 5.62 score 5 scripts

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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.

immunooncology software singlecell onechannel twochannel multichannel spatial dataimport bioconductor imaging shiny visualization

7 stars 5.50 score 15 scripts

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tilingArray:Transcript mapping with high-density oligonucleotide tiling arrays

The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class 'segmentation' for representing partitionings of a linear series of data; 2. the function 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function 'confint' for calculating confidence intervals using the strucchange package; 4. the function 'plotAlongChrom' for generating pretty plots; 5. the function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.

Maintained by Zhenyu Xu. Last updated 5 months ago.

microarray onechannel preprocessing visualization

5.48 score 5 scripts 1 dependents

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

This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package.

Maintained by Adi L. Tarca. Last updated 2 months ago.

microarray onechannel twochannel

5.46 score 12 scripts 2 dependents

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PROMISE:PRojection Onto the Most Interesting Statistical Evidence

A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019

Maintained by Stan Pounds. Last updated 5 months ago.

microarray onechannel multiplecomparison geneexpression

5.44 score 46 scripts 1 dependents

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GlobalAncova:Global test for groups of variables via model comparisons

The association between a variable of interest (e.g. two groups) and the global pattern of a group of variables (e.g. a gene set) is tested via a global F-test. We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. The framework is generalized to groups of categorical variables or even mixed data by a likelihood ratio approach. Closed and hierarchical testing procedures are supported. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany and BMBF grant 01ZX1309B, Germany.

Maintained by Manuela Hummel. Last updated 5 months ago.

microarray onechannel differentialexpression pathways regression

5.31 score 9 scripts 1 dependents

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altcdfenvs:alternative CDF environments (aka probeset mappings)

Convenience data structures and functions to handle cdfenvs

Maintained by Laurent Gautier. Last updated 5 months ago.

microarray onechannel qualitycontrol preprocessing annotation proprietaryplatforms transcription

4.95 score 5 scripts 1 dependents

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AMARETTO:Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

Integrating an increasing number of available multi-omics cancer data remains one of the main challenges to improve our understanding of cancer. One of the main challenges is using multi-omics data for identifying novel cancer driver genes. We have developed an algorithm, called AMARETTO, that integrates copy number, DNA methylation and gene expression data to identify a set of driver genes by analyzing cancer samples and connects them to clusters of co-expressed genes, which we define as modules. We applied AMARETTO in a pancancer setting to identify cancer driver genes and their modules on multiple cancer sites. AMARETTO captures modules enriched in angiogenesis, cell cycle and EMT, and modules that accurately predict survival and molecular subtypes. This allows AMARETTO to identify novel cancer driver genes directing canonical cancer pathways.

Maintained by Olivier Gevaert. Last updated 5 months ago.

statisticalmethod differentialmethylation generegulation geneexpression methylationarray transcription preprocessing batcheffect dataimport mrnamicroarray micrornaarray regression clustering rnaseq copynumbervariation sequencing microarray normalization network bayesian exonarray onechannel twochannel proprietaryplatforms alternativesplicing differentialexpression differentialsplicing genesetenrichment multiplecomparison qualitycontrol timecourse

4.88 score 15 scripts

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puma:Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.

Maintained by Xuejun Liu. Last updated 8 days ago.

microarray onechannel preprocessing differentialexpression clustering exonarray geneexpression mrnamicroarray chiponchip alternativesplicing differentialsplicing bayesian twochannel dataimport hta2.0

4.71 score 17 scripts

bioc

affylmGUI:GUI for limma Package with Affymetrix Microarrays

A Graphical User Interface (GUI) for analysis of Affymetrix microarray gene expression data using the affy and limma packages.

Maintained by Gordon Smyth. Last updated 5 months ago.

gui geneexpression transcription differentialexpression dataimport bayesian regression timecourse microarray mrnamicroarray onechannel proprietaryplatforms batcheffect multiplecomparison normalization preprocessing qualitycontrol

4.60 score 3 scripts

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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.

microarray onechannel twochannel multichannel differentialexpression exonarray geneexpression transcription multiplecomparison preprocessing qualitycontrol

4.41 score 64 scripts

bioc

PAA:PAA (Protein Array Analyzer)

PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.

Maintained by Michael Turewicz. Last updated 5 months ago.

classification microarray onechannel proteomics cpp

4.34 score 11 scripts

samarafk

MLML2R:Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions

Maximum likelihood estimates (MLE) of the proportions of 5-mC and 5-hmC in the DNA using information from BS-conversion, TAB-conversion, and oxBS-conversion methods. One can use information from all three methods or any combination of two of them. Estimates are based on Binomial model by Qu et al. (2013) <doi:10.1093/bioinformatics/btt459> and Kiihl et al. (2019) <doi:10.1515/sagmb-2018-0031>.

Maintained by Samara Kiihl. Last updated 5 years ago.

software methylationarray epigenetics dnamethylation microarray twochannel onechannel

2 stars 4.34 score 22 scripts

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

The MSstatsLOBD package allows calculation and visualization of limit of blac (LOB) and limit of detection (LOD). We define the LOB as the highest apparent concentration of a peptide expected when replicates of a blank sample containing no peptides are measured. The LOD is defined as the measured concentration value for which the probability of falsely claiming the absence of a peptide in the sample is 0.05, given a probability 0.05 of falsely claiming its presence. These functionalities were previously a part of the MSstats package. The methodology is described in Galitzine (2018) <doi:10.1074/mcp.RA117.000322>.

Maintained by Devon Kohler. Last updated 5 months ago.

immunooncology massspectrometry proteomics software differentialexpression onechannel twochannel normalization qualitycontrol mass-spectrometry

4.30 score 1 scripts

bioc

CAFE:Chromosmal Aberrations Finder in Expression data

Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input

Maintained by Sander Bollen. Last updated 5 months ago.

geneexpression microarray onechannel genesetenrichment

4.30 score 2 scripts

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cyanoFilter:Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

An approach to filter out and/or identify phytoplankton cells from all particles measured via flow cytometry pigment and cell complexity information. It does this using a sequence of one-dimensional gates on pre-defined channels measuring certain pigmentation and complexity. The package is especially tuned for cyanobacteria, but will work fine for phytoplankton communities where there is at least one cell characteristic that differentiates every phytoplankton in the community.

Maintained by Oluwafemi Olusoji. Last updated 5 months ago.

flowcytometry clustering onechannel

4.30 score 4 scripts

bioc

protGear:Protein Micro Array Data Management and Interactive Visualization

A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.

Maintained by Kennedy Mwai. Last updated 5 months ago.

microarray onechannel preprocessing biomedicalinformatics proteomics batcheffect normalization bayesian clustering regression systemsbiology immunooncology background-correction microarray-data normalisation proteomics-data shiny shinydashboard

1 stars 4.30 score 6 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.

microarray onechannel twochannel multichannel dataimport datarepresentation gui visualization preprocessing qualitycontrol acgh copynumbervariants

1 stars 4.30 score 16 scripts 6 dependents

bioc

gaga:GaGa hierarchical model for high-throughput data analysis

Implements the GaGa model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample size calculations using the GaGa and LNNGV models (the latter from EBarrays package).

Maintained by David Rossell. Last updated 1 months ago.

immunooncology onechannel massspectrometry multiplecomparison differentialexpression classification

4.26 score 9 scripts 1 dependents

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

Automated pipline to perform gene expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A GUI interface is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.

Maintained by Yongming Andrew Sun. Last updated 5 months ago.

microarray onechannel preprocessing

4.20 score 3 scripts

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Harshlight:A "corrective make-up" program for microarray chips

The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.

Maintained by Maurizio Pellegrino. Last updated 5 months ago.

microarray qualitycontrol preprocessing onechannel reportwriting

4.20 score 2 scripts

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codelink:Manipulation of Codelink microarray data

This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.

Maintained by Diego Diez. Last updated 5 months ago.

microarray onechannel dataimport preprocessing

4.20 score 5 scripts

bioc

iChip:Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models

Hidden Ising models are implemented to identify enriched genomic regions in ChIP-chip data. They can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates.

Maintained by Qianxing Mo. Last updated 5 months ago.

chipchip onechannel agilentchip microarray

4.15 score 3 scripts

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

The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

Maintained by Mario Fasold. Last updated 5 months ago.

geneexpression microarray onechannel preprocessing qualitycontrol

4.08 score 2 scripts

bioc

cytoKernel:Differential expression using kernel-based score test

cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression data. In this R package, we implement functions that compute the feature-wise p values and their corresponding adjusted p values. Additionally, it also computes the feature-wise shrunk effect sizes and their corresponding shrunken effect size. Further, it calculates the percent of differentially expressed features and plots user-friendly heatmap of the top differentially expressed features on the rows and samples on the columns.

Maintained by Tusharkanti Ghosh. Last updated 5 months ago.

immunooncology proteomics singlecell software onechannel flowcytometry differentialexpression geneexpression clustering cpp

4.00 score 4 scripts

bioc

webbioc:Bioconductor Web Interface

An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. (Currently only Affymetrix oligonucleotide analysis is supported.)

Maintained by Colin A. Smith. Last updated 5 months ago.

infrastructure microarray onechannel differentialexpression

3.90 score 4 scripts

bioc

RLMM:A Genotype Calling Algorithm for Affymetrix SNP Arrays

A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.

Maintained by Nusrat Rabbee. Last updated 5 months ago.

microarray onechannel snp geneticvariability

3.90 score 1 scripts

bioc

lmdme:Linear Model decomposition for Designed Multivariate Experiments

linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i)Flexible formula type interface, ii) Fast limma based implementation, iii) p-values for each estimated coefficient levels in each factor, iv) F values for factor effects and v) plotting functions for PCA and PLS.

Maintained by Cristobal Fresno. Last updated 5 months ago.

microarray onechannel twochannel visualization differentialexpression experimentdata cancer

3.78 score 1 scripts

bioc

GeneRegionScan:GeneRegionScan

A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.

Maintained by Lasse Folkersen. Last updated 5 months ago.

microarray dataimport snp onechannel visualization

3.78 score 1 scripts

bioc

copa:Functions to perform cancer outlier profile analysis.

COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles.

Maintained by James W. MacDonald. Last updated 5 months ago.

onechannel twochannel differentialexpression visualization

3.60 score 2 scripts

bioc

affyILM:Linear Model of background subtraction and the Langmuir isotherm

affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model.

Maintained by Myriam Kroll and Fabrice Berger. Last updated 5 months ago.

microarray onechannel preprocessing

3.60 score 1 scripts

bioc

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

SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.

Maintained by Stephen R. Piccolo. Last updated 5 months ago.

immunooncology software microarray preprocessing rnaseq twochannel onechannel

3.48 score 15 scripts

bioc

SNAGEE:Signal-to-Noise applied to Gene Expression Experiments

Signal-to-Noise applied to Gene Expression Experiments. Signal-to-noise ratios can be used as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set.

Maintained by David Venet. Last updated 5 months ago.

microarray onechannel twochannel qualitycontrol

3.30 score 3 scripts

bioc

TurboNorm:A fast scatterplot smoother suitable for microarray normalization

A fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.

Maintained by Maarten van Iterson. Last updated 5 months ago.

microarray onechannel twochannel preprocessing dnamethylation cpgisland methylationarray normalization

3.30 score 1 scripts

bioc

clippda:A package for the clinical proteomic profiling data analysis

Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.

Maintained by Stephen Nyangoma. Last updated 5 months ago.

proteomics onechannel preprocessing differentialexpression multiplecomparison

3.30 score 2 scripts

henrikbengtsson

ACNE:Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).

Maintained by Henrik Bengtsson. Last updated 1 years ago.

acgh copynumbervariants snp microarray onechannel twochannel genetics

3.18 score 2 scripts

bioc

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

annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl. The annmap database can be downloaded from: https://figshare.manchester.ac.uk/account/articles/16685071

Maintained by Chris Wirth. Last updated 5 months ago.

annotation microarray onechannel reportwriting transcription visualization

3.00 score 2 scripts

bioc

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.

geneexpression differentialexpression microarray preprocessing dnamethylation onechannel twochannel qualitycontrol

3.00 score 1 scripts

bioc

ExiMiR:R functions for the normalization of Exiqon miRNA array data

This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.

Maintained by Sylvain Gubian. Last updated 5 months ago.

microarray onechannel twochannel preprocessing geneexpression transcription

2.78 score 3 scripts

henrikbengtsson

aroma.cn:Copy-Number Analysis of Large Microarray Data Sets

Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

proprietaryplatforms acgh copynumbervariants snp microarray onechannel twochannel dataimport datarepresentation preprocessing qualitycontrol

1 stars 2.70 score 9 scripts

henrikbengtsson

calmate:Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

The CalMaTe method calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. The resulting ASCNs are on average more accurate, which increases the power of segmentation methods for detecting changes between copy number states in tumor studies including copy neutral loss of heterozygosity. CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. Affymetrix and Illumina.

Maintained by Henrik Bengtsson. Last updated 3 years ago.

acgh copynumbervariants snp microarray onechannel twochannel genetics

1 stars 2.70 score 6 scripts

bioc

roastgsa:Rotation based gene set analysis

This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.

Maintained by Adria Caballe. Last updated 5 months ago.

microarray preprocessing normalization geneexpression survival transcription sequencing transcriptomics bayesian clustering regression rnaseq micrornaarray mrnamicroarray functionalgenomics systemsbiology immunooncology differentialexpression genesetenrichment batcheffect multiplecomparison qualitycontrol timecourse metabolomics proteomics epigenetics cheminformatics exonarray onechannel twochannel proprietaryplatforms cellbiology biomedicalinformatics alternativesplicing differentialsplicing dataimport pathways

2.30 score

bioc

pvac:PCA-based gene filtering for Affymetrix arrays

The package contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).

Maintained by Jun Lu. Last updated 5 months ago.

microarray onechannel qualitycontrol

2.30 score 2 scripts