Showing 82 of total 82 results (show query)
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.
infrastructureproprietaryplatformsexonarraymicroarrayonechannelguidataimportdatarepresentationpreprocessingqualitycontrolvisualizationreportwritingacghcopynumbervariantsdifferentialexpressiongeneexpressionsnptranscriptionaffymetrixanalysiscopy-numberdnaexpressionhpclarge-scalenotebookreproducibilityrna
57.8 match 10 stars 5.79 score 112 scripts 3 dependents
bioc
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 2 months ago.
infrastructuredataimportmicroarrayproprietaryplatformsonechannelbioconductorcpp
33.3 match 7 stars 8.19 score 65 scripts 14 dependentsbioc
annotate:Annotation for microarrays
Using R enviroments for annotation.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
17.4 match 11.41 score 812 scripts 243 dependentsbioc
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 2 months ago.
microarrayonechannelpreprocessing
10.3 match 11.12 score 2.5k scripts 98 dependentshenrikbengtsson
aroma.apd:A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]
DEPRECATED. Do not start building new projects based on this package. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speeds up the read substantially. This package is supporting the Aroma framework and should not be used elsewhere.)
Maintained by Henrik Bengtsson. Last updated 2 years ago.
22.3 match 3.82 score 11 scripts 4 dependentsbioc
ROTS:Reproducibility-Optimized Test Statistic
Calculates the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.
Maintained by Tomi Suomi. Last updated 2 months ago.
softwaregeneexpressiondifferentialexpressionmicroarrayrnaseqproteomicsimmunooncologycpp
8.8 match 6.73 score 86 scripts 3 dependentsbioc
BgeeDB:Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.
Maintained by Julien Wollbrett. Last updated 5 months ago.
softwaredataimportsequencinggeneexpressionmicroarraygogenesetenrichmentbioinformaticsenrichment-analysisrna-seqscrna-seqsingle-cell
5.0 match 15 stars 8.46 score 19 scripts 1 dependentsbioc
genefilter:genefilter: methods for filtering genes from high-throughput experiments
Some basic functions for filtering genes.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
3.5 match 11.10 score 2.4k scripts 142 dependentsbioc
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 12 days ago.
microarraypreprocessingsnpcopynumbervariation
8.1 match 4.78 score 37 scripts 3 dependents
cbiit
LDlinkR:Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest
Provides access to the 'LDlink' API (<https://ldlink.nih.gov/?tab=apiaccess>) using the R console. This programmatic access facilitates researchers who are interested in performing batch queries in 1000 Genomes Project (2015) <doi:10.1038/nature15393> data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying germline variants in human population groups of interest. For more details, please see Machiela et al. (2015) <doi:10.1093/bioinformatics/btv402>.
Maintained by Timothy A. Myers. Last updated 11 months ago.
ld-calculatorldlinkldlink-apildlink-webtoollinkage-disequilibriumpopulation-genetics
3.8 match 58 stars 9.21 score 206 scripts 1 dependentsbioc
GWASTools:Tools for Genome Wide Association Studies
Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.
Maintained by Stephanie M. Gogarten. Last updated 5 months ago.
snpgeneticvariabilityqualitycontrolmicroarray
3.3 match 17 stars 10.50 score 396 scripts 5 dependentsbioc
biomaRt:Interface to BioMart databases (i.e. Ensembl)
In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<http://www.biomart.org>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.
Maintained by Mike Smith. Last updated 2 days ago.
annotationbioconductorbiomartensembl
2.2 match 38 stars 15.99 score 13k scripts 230 dependentsbioc
consensus:Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
An implementation of the American Society for Testing and Materials (ASTM) Standard E691 for interlaboratory testing procedures, designed for cross-platform genomic measurements. Given three (3) or more genomic platforms or laboratory protocols, this package provides interlaboratory testing procedures giving per-locus comparisons for sensitivity and precision between platforms.
Maintained by Tim Peters. Last updated 5 months ago.
qualitycontrolregressiondatarepresentationgeneexpressionmicroarrayrnaseq
7.2 match 4.70 score 10 scriptsbioc
AnnotationForge:Tools for building SQLite-based annotation data packages
Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.
Maintained by Bioconductor Package Maintainer. Last updated 3 days ago.
annotationinfrastructurebioconductor-packagecore-package
3.5 match 5 stars 9.62 score 143 scripts 19 dependentsbioc
annotationTools:Annotate microarrays and perform cross-species gene expression analyses using flat file databases
Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).
Maintained by Alexandre Kuhn. Last updated 5 months ago.
7.2 match 4.51 score 18 scripts 1 dependentsbioc
affyio:Tools for parsing Affymetrix data files
Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.
Maintained by Ben Bolstad. Last updated 2 months ago.
microarraydataimportinfrastructurezlib
3.5 match 3 stars 8.94 score 40 scripts 110 dependentsbioc
rCGH:Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.
Maintained by Frederic Commo. Last updated 5 months ago.
acghcopynumbervariationpreprocessingfeatureextraction
5.9 match 4 stars 5.10 score 26 scripts 1 dependentsbioc
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.
onechannelmicroarraypreprocessing
5.0 match 5.92 score 14 scripts
tinnlab
RCPA:Consensus Pathway Analysis
Provides a set of functions to perform pathway analysis and meta-analysis from multiple gene expression datasets, as well as visualization of the results. This package wraps functionality from the following packages: Ritchie et al. (2015) <doi:10.1093/nar/gkv007>, Love et al. (2014) <doi:10.1186/s13059-014-0550-8>, Robinson et al. (2010) <doi:10.1093/bioinformatics/btp616>, Korotkevich et al. (2016) <arxiv:10.1101/060012>, Efron et al. (2015) <https://CRAN.R-project.org/package=GSA>, and Gu et al. (2012) <https://CRAN.R-project.org/package=CePa>.
Maintained by Ha Nguyen. Last updated 4 months ago.
biobasedeseq2geoqueryedgerlimmarcyjsfgseabrowservizsummarizedexperimentannotationdbirontotools
5.4 match 1 stars 5.50 score 70 scriptsbioc
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.
reportwritingmicroarrayonechannelgeneexpression
4.8 match 6.07 score 117 scriptsbioc
CINdex:Chromosome Instability Index
The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.
Maintained by Yuriy Gusev. Last updated 5 months ago.
softwarecopynumbervariationgenomicvariationacghmicroarraygeneticssequencing
7.1 match 4.08 score 2 scriptsbioc
mBPCR:Bayesian Piecewise Constant Regression for DNA copy number estimation
It contains functions for estimating the DNA copy number profile using mBPCR with the aim of detecting regions with copy number changes.
Maintained by P.M.V. Rancoita. Last updated 5 months ago.
acghsnpmicroarraycopynumbervariation
6.5 match 3.90 score 1 scripts
kaiaragaki
tidyestimate:A Tidy Implementation of 'ESTIMATE'
The 'ESTIMATE' package infers tumor purity from expression data as a function of immune and stromal infiltrate, but requires writing of intermediate files, is un-pipeable, and performs poorly when presented with modern datasets with current gene symbols. 'tidyestimate' a fast, tidy, modern reimagination of 'ESTIMATE' (2013) <doi:10.1038/ncomms3612>.
Maintained by Kai Aragaki. Last updated 2 years ago.
5.2 match 14 stars 4.85 score 4 scriptsbioc
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.
microarrayonechannelpreprocessingqualitycontrolopenblaszlib
3.5 match 6.99 score 206 scripts 4 dependentsbioc
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.
guigeneexpressiontranscriptiondifferentialexpressiondataimportbayesianregressiontimecoursemicroarraymrnamicroarrayonechannelproprietaryplatformsbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrol
5.2 match 4.60 score 3 scriptsbioc
Mulcom:Calculates Mulcom test
Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test.
Maintained by Claudio Isella. Last updated 5 months ago.
statisticalmethodmultiplecomparisonmicroarraydifferentialexpressiongeneexpressioncpp
7.2 match 3.00 scorebioc
plier:Implements the Affymetrix PLIER algorithm
The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.
Maintained by Crispin Miller. Last updated 5 months ago.
4.9 match 4.14 score 115 scriptsbioc
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.
onechannelmicroarrayannotationgopathwaysreportwriting
3.5 match 5.64 score 60 scripts 3 dependents
holgerschw
scrime:Analysis of High-Dimensional Categorical Data Such as SNP Data
Tools for the analysis of high-dimensional data developed/implemented at the group "Statistical Complexity Reduction In Molecular Epidemiology" (SCRIME). Main focus is on SNP data. But most of the functions can also be applied to other types of categorical data.
Maintained by Holger Schwender. Last updated 6 years ago.
3.7 match 4.98 score 53 scripts 34 dependentsbioc
spikeLI:Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006).
Maintained by Enrico Carlon. Last updated 5 months ago.
5.4 match 3.30 score
cran
jetset:One-to-One Gene-Probeset Mapping for Affymetrix Human Microarrays
On Affymetrix gene expression microarrays, a single gene may be measured by multiple probe sets. This can present a mild conundrum when attempting to evaluate a gene "signature" that is defined by gene names rather than by specific probe sets. This package provides a one-to-one mapping from gene to "best" probe set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a, hgu133plus2, and u133x3p. This package also includes the pre-calculated probe set quality scores that were used to define the mapping.
Maintained by Aron Eklund. Last updated 8 years ago.
3.6 match 4.75 score 47 scripts 1 dependents
natydasilva
PPforest:Projection Pursuit Classification Forest
Implements projection pursuit forest algorithm for supervised classification.
Maintained by Natalia da Silva. Last updated 8 months ago.
3.0 match 18 stars 5.53 score 19 scriptsbioc
ITALICS:ITALICS
A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set
Maintained by Guillem Rigaill. Last updated 5 months ago.
4.1 match 4.08 scorebioc
goTools:Functions for Gene Ontology database
Wraper functions for description/comparison of oligo ID list using Gene Ontology database
Maintained by Agnes Paquet. Last updated 5 months ago.
4.9 match 3.30 score 1 scriptsbioc
DTA:Dynamic Transcriptome Analysis
Dynamic Transcriptome Analysis (DTA) can monitor the cellular response to perturbations with higher sensitivity and temporal resolution than standard transcriptomics. The package implements the underlying kinetic modeling approach capable of the precise determination of synthesis- and decay rates from individual microarray or RNAseq measurements.
Maintained by Bjoern Schwalb. Last updated 5 months ago.
microarraydifferentialexpressiongeneexpressiontranscription
3.4 match 4.78 score 5 scripts 1 dependents
gitumino
fitPoly:Genotype Calling for Bi-Allelic Marker Assays
Genotyping assays for bi-allelic markers (e.g. SNPs) produce signal intensities for the two alleles. 'fitPoly' assigns genotypes (allele dosages) to a collection of polyploid samples based on these signal intensities. 'fitPoly' replaces the older package 'fitTetra' that was limited (a.o.) to only tetraploid populations whereas 'fitPoly' accepts any ploidy level. Reference: Voorrips RE, Gort G, Vosman B (2011) <doi:10.1186/1471-2105-12-172>. New functions added on conversion of data from SNP array software formats, drawing of XY-scatterplots with or without genotype colors, checking against expected F1 segregation patterns, comparing results from two different assays (probes) for the same SNP, recovery from a saveMarkerModels() crash.
Maintained by Giorgio Tumino. Last updated 1 months ago.
3.9 match 4.13 score 15 scriptsbioc
GeneMeta:MetaAnalysis for High Throughput Experiments
A collection of meta-analysis tools for analysing high throughput experimental data
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
sequencinggeneexpressionmicroarray
3.3 match 4.78 score 2 scripts 1 dependentsbioc
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 5 months ago.
microarrayonechannelpreprocessingdifferentialexpressionclusteringexonarraygeneexpressionmrnamicroarraychiponchipalternativesplicingdifferentialsplicingbayesiantwochanneldataimporthta2.0
3.4 match 4.53 score 17 scriptsbioc
a4Base:Automated Affymetrix Array Analysis Base Package
Base utility functions are available for the Automated Affymetrix Array Analysis set of packages.
Maintained by Laure Cougnaud. Last updated 5 months ago.
5.2 match 2.92 score 14 scripts 1 dependentsbioc
a4Core:Automated Affymetrix Array Analysis Core Package
Utility functions for the Automated Affymetrix Array Analysis set of packages.
Maintained by Laure Cougnaud. Last updated 5 months ago.
3.5 match 4.38 score 2 scripts 4 dependentsbioc
a4Preproc:Automated Affymetrix Array Analysis Preprocessing Package
Utility functions to pre-process data for the Automated Affymetrix Array Analysis set of packages.
Maintained by Laure Cougnaud. Last updated 5 months ago.
3.5 match 4.26 score 4 scripts 3 dependentsbioc
a4Classif:Automated Affymetrix Array Analysis Classification Package
Functionalities for classification of Affymetrix microarray data, integrating within the Automated Affymetrix Array Analysis set of packages.
Maintained by Laure Cougnaud. Last updated 5 months ago.
microarraygeneexpressionclassification
3.8 match 3.78 score 1 scripts 1 dependentsbioc
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 2 months ago.
onechanneldataimportpreprocessingzlib
2.3 match 5.81 score 36 scripts 2 dependentsbioc
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.
microarrayonechannelsnpgeneticvariability
3.4 match 3.90 score 1 scriptsbioc
pdInfoBuilder:Platform Design Information Package Builder
Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.
Maintained by Benilton Carvalho. Last updated 5 months ago.
2.9 match 4.49 score 13 scriptsbioc
a4Reporting:Automated Affymetrix Array Analysis Reporting Package
Utility functions to facilitate the reporting of the Automated Affymetrix Array Analysis Reporting set of packages.
Maintained by Laure Cougnaud. Last updated 5 months ago.
3.5 match 3.78 score 3 scripts 1 dependentsbioc
a4:Automated Affymetrix Array Analysis Umbrella Package
Umbrella package is available for the entire Automated Affymetrix Array Analysis suite of package.
Maintained by Laure Cougnaud. Last updated 5 months ago.
3.5 match 3.65 score 15 scriptsbioc
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.
microarrayonechannelpreprocessingvisualization
2.2 match 5.48 score 5 scripts 1 dependentsbioc
autonomics:Unified Statistical Modeling of Omics Data
This package unifies access to Statistal Modeling of Omics Data. Across linear modeling engines (lm, lme, lmer, limma, and wilcoxon). Across coding systems (treatment, difference, deviation, etc). Across model formulae (with/without intercept, random effect, interaction or nesting). Across omics platforms (microarray, rnaseq, msproteomics, affinity proteomics, metabolomics). Across projection methods (pca, pls, sma, lda, spls, opls). Across clustering methods (hclust, pam, cmeans). It provides a fast enrichment analysis implementation. And an intuitive contrastogram visualisation to summarize contrast effects in complex designs.
Maintained by Aditya Bhagwat. Last updated 2 months ago.
softwaredataimportpreprocessingdimensionreductionprincipalcomponentregressiondifferentialexpressiongenesetenrichmenttranscriptomicstranscriptiongeneexpressionrnaseqmicroarrayproteomicsmetabolomicsmassspectrometry
2.0 match 5.95 score 5 scriptsbioc
spkTools:Methods for Spike-in Arrays
The package contains functions that can be used to compare expression measures on different array platforms.
Maintained by Matthew N McCall. Last updated 5 months ago.
3.6 match 3.30 score 1 scriptsbioc
Repitools:Epigenomic tools
Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.
Maintained by Mark Robinson. Last updated 5 months ago.
dnamethylationgeneexpressionmethylseq
1.8 match 5.90 score 267 scriptsbioc
oligoClasses:Classes for high-throughput arrays supported by oligo and crlmm
This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.
Maintained by Benilton Carvalho. Last updated 5 months ago.
1.8 match 5.85 score 93 scripts 17 dependentshenrikbengtsson
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.
acghcopynumbervariantssnpmicroarrayonechanneltwochannelgenetics
3.3 match 3.18 score 2 scriptsbioc
EventPointer:An effective identification of alternative splicing events using junction arrays and RNA-Seq data
EventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3',...,etc), genomic position, statistical significance and increment of the percent spliced in (Delta PSI) for all the events. The algorithm can generate a series of files to visualize the detected alternative splicing events in IGV. This eases the interpretation of results and the design of primers for standard PCR validation.
Maintained by Juan A. Ferrer-Bonsoms. Last updated 5 months ago.
alternativesplicingdifferentialsplicingmrnamicroarrayrnaseqtranscriptionsequencingtimecourseimmunooncology
1.7 match 4 stars 6.00 score 6 scriptsbioc
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.
annotationmicroarrayonechannelreportwritingtranscriptionvisualization
3.3 match 3.00 score 2 scripts
mpierrejean
jointseg:Joint Segmentation of Multivariate (Copy Number) Signals
Methods for fast segmentation of multivariate signals into piecewise constant profiles and for generating realistic copy-number profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies. The methods are described in Pierre-Jean, Rigaill and Neuvial (2015) <doi:10.1093/bib/bbu026>.
Maintained by Morgane Pierre-Jean. Last updated 6 years ago.
1.5 match 6 stars 6.50 score 44 scripts 2 dependentsbioc
affyContam:structured corruption of affymetrix cel file data
structured corruption of cel file data to demonstrate QA effectiveness
Maintained by V. Carey. Last updated 5 months ago.
2.9 match 3.30 score 1 scriptsbioc
altcdfenvs:alternative CDF environments (aka probeset mappings)
Convenience data structures and functions to handle cdfenvs
Maintained by Laurent Gautier. Last updated 5 months ago.
microarrayonechannelqualitycontrolpreprocessingannotationproprietaryplatformstranscription
1.9 match 4.95 score 5 scripts 1 dependentsbioc
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.
immunooncologysoftwaremicroarraypreprocessingrnaseqtwochannelonechannel
2.1 match 3.48 score 15 scriptsbioc
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.
microarrayonechannelqualitycontrol
2.9 match 2.30 score 2 scripts
bioc
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 8 days ago.
microarrayonechanneltwochannelpreprocessingsnpdifferentialexpressionexonarraygeneexpressiondataimportzlib
0.5 match 3 stars 10.42 score 528 scripts 10 dependentsbioc
bgx:Bayesian Gene eXpression
Bayesian integrated analysis of Affymetrix GeneChips
Maintained by Ernest Turro. Last updated 5 months ago.
microarraydifferentialexpressioncppglibc
2.3 match 2.30 score 1 scriptsbioc
BioNet:Routines for the functional analysis of biological networks
This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.
Maintained by Marcus Dittrich. Last updated 5 months ago.
microarraydataimportgraphandnetworknetworknetworkenrichmentgeneexpressiondifferentialexpression
0.5 match 6.14 score 114 scripts 2 dependents
jmzeng1314
AnnoProbe:annotate the gene symbols for probes in expression array
We curated 147 of expression array, from 3 species(human,mouse,rat), 3 companies(affymetrix,illumina,agilent), by aligning the fasta sequences of all probes of each platform to their corresponding reference genome, and then annotate them to genes.
Maintained by The package maintainer. Last updated 5 years ago.
0.5 match 104 stars 5.82 score 126 scriptsbioc
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.
microarraydataimportsnponechannelvisualization
0.8 match 3.78 score 1 scriptsbioc
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.
geneexpressionmicroarrayonechannelgenesetenrichment
0.6 match 4.30 score 2 scriptsbioc
IntramiRExploreR:Predicting Targets for Drosophila Intragenic miRNAs
Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using the tool, we have identified targets for 92 intragenic miRs in D. melanogaster, using available microarray expression data, from Affymetrix 1 and Affymetrix2 microarray array platforms, providing a global perspective of intragenic miR targets in Drosophila. Predicted targets are grouped according to biological functions using the DAVID Gene Ontology tool and are ranked based on a biologically relevant scoring system, enabling the user to identify functionally relevant targets for a given miR.
Maintained by Surajit Bhattacharya. Last updated 5 months ago.
softwaremicroarraygenetargetstatisticalmethodgeneexpressiongeneprediction
0.5 match 4.60 score 4 scriptsbioc
PECA:Probe-level Expression Change Averaging
Calculates Probe-level Expression Change Averages (PECA) to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively.
Maintained by Tomi Suomi. Last updated 5 months ago.
softwareproteomicsmicroarraydifferentialexpressiongeneexpressionexonarraydifferentialsplicing
0.5 match 4.34 score 11 scriptshenrikbengtsson
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
0.5 match 1 stars 4.30 score 16 scripts 6 dependentsbioc
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.
chipchiponechannelagilentchipmicroarray
0.5 match 4.15 score 3 scriptsbioc
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.
geneexpressionmicroarrayonechannelpreprocessingqualitycontrol
0.5 match 4.08 score 2 scriptsbioc
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.
infrastructuremicroarrayonechanneldifferentialexpression
0.5 match 3.90 score 4 scriptsbioc
CellScore:Tool for Evaluation of Cell Identity from Transcription Profiles
The CellScore package contains functions to evaluate the cell identity of a test sample, given a cell transition defined with a starting (donor) cell type and a desired target cell type. The evaluation is based upon a scoring system, which uses a set of standard samples of known cell types, as the reference set. The functions have been carried out on a large set of microarray data from one platform (Affymetrix Human Genome U133 Plus 2.0). In principle, the method could be applied to any expression dataset, provided that there are a sufficient number of standard samples and that the data are normalized.
Maintained by Nancy Mah. Last updated 5 months ago.
geneexpressiontranscriptionmicroarraymultiplecomparisonreportwritingdataimportvisualization
0.5 match 4.00 score 5 scriptshenrikbengtsson
R.huge:Methods for Accessing Huge Amounts of Data [deprecated]
DEPRECATED. Do not start building new projects based on this package. Cross-platform alternatives are the following packages: bigmemory (CRAN), ff (CRAN), BufferedMatrix (Bioconductor). The main usage of it was inside the aroma.affymetrix package. (The package currently provides a class representing a matrix where the actual data is stored in a binary format on the local file system. This way the size limit of the data is set by the file system and not the memory.)
Maintained by Henrik Bengtsson. Last updated 1 years ago.
0.5 match 3.88 score 2 scripts 5 dependentsbioc
panp:Presence-Absence Calls from Negative Strand Matching Probesets
A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.
Maintained by Peter Warren. Last updated 5 months ago.
0.5 match 3.78 score 2 scriptsbioc
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.
microarrayonechannelpreprocessing
0.5 match 3.60 score 1 scriptsbioc
cn.farms:cn.FARMS - factor analysis for copy number estimation
This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0) array types, supports high-performance computing using snow and ff.
Maintained by Andreas Mitterecker. Last updated 5 months ago.
microarraycopynumbervariationcpp
0.5 match 3.30 score 7 scriptsbioc
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.
microarrayonechanneltwochannelpreprocessingdnamethylationcpgislandmethylationarraynormalization
0.5 match 3.30 score 1 scriptscran
BioVenn:Create Area-Proportional Venn Diagrams from Biological Lists
Creates an area-proportional Venn diagram of 2 or 3 circles. 'BioVenn' is the only R package that can automatically generate an accurate area-proportional Venn diagram by having only lists of (biological) identifiers as input. Also offers the option to map Entrez and/or Affymetrix IDs to Ensembl IDs. In SVG mode, text and numbers can be dragged and dropped. Based on the BioVenn web interface available at <https://www.biovenn.nl>. Hulsen (2021) <doi:10.3233/DS-210032>.
Maintained by Tim Hulsen. Last updated 4 years ago.
0.5 match 1 stars 3.00 scorehenrikbengtsson
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.
acghcopynumbervariantssnpmicroarrayonechanneltwochannelgenetics
0.5 match 1 stars 2.70 score 6 scripts
dhammapalb
maGUI:A Graphical User Interface for Microarray Data Analysis and Annotation
Provides a comprehensive graphical user interface for analysis of Affymetrix, Agilent, Illumina, Nimblegen and other microarray data. It can perform miscellaneous tasks such as gene set enrichment and test analyses, identifying gene symbols and building co-expression network. It can also estimate sample size for atleast two-fold expression change. The current version is its slenderized form for compatable and flexible implementation.
Maintained by Dhammapal Bharne. Last updated 3 years ago.
0.5 match 1.00 score