Showing 13 of total 13 results (show query)
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 12 days ago.
exonarraygeneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentdataimportbayesianclusteringregressiontimecoursemicroarraymicrornaarraymrnamicroarrayonechannelproprietaryplatformstwochannelsequencingrnaseqbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrolbiomedicalinformaticscellbiologycheminformaticsepigeneticsfunctionalgenomicsgeneticsimmunooncologymetabolomicsproteomicssystemsbiologytranscriptomics
13.81 score 16k scripts 586 dependentsbioc
illuminaio:Parsing Illumina Microarray Output Files
Tools for parsing Illumina's microarray output files, including IDAT.
Maintained by Kasper Daniel Hansen. Last updated 5 months ago.
infrastructuredataimportmicroarrayproprietaryplatformsbioconductor
5 stars 10.28 score 58 scripts 37 dependentsbioc
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.
infrastructuredataimportmicroarrayproprietaryplatformsonechannelbioconductorcpp
7 stars 8.19 score 65 scripts 14 dependentsbioc
GeomxTools:NanoString GeoMx Tools
Tools for NanoString Technologies GeoMx Technology. Package provides functions for reading in DCC and PKC files based on an ExpressionSet derived object. Normalization and QC functions are also included.
Maintained by Maddy Griswold. Last updated 5 months ago.
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseqsequencingexperimentaldesignnormalizationspatial
7.11 score 239 scripts 3 dependentsbioc
NanoStringNCTools:NanoString nCounter Tools
Tools for NanoString Technologies nCounter Technology. Provides support for reading RCC files into an ExpressionSet derived object. Also includes methods for QC and normalizaztion of NanoString data.
Maintained by Maddy Griswold. Last updated 5 months ago.
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsmrnamicroarrayproprietaryplatformsrnaseq
6.35 score 94 scripts 4 dependentsbioc
metaseqR2:An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.
Maintained by Panagiotis Moulos. Last updated 19 days ago.
softwaregeneexpressiondifferentialexpressionworkflowsteppreprocessingqualitycontrolnormalizationreportwritingrnaseqtranscriptionsequencingtranscriptomicsbayesianclusteringcellbiologybiomedicalinformaticsfunctionalgenomicssystemsbiologyimmunooncologyalternativesplicingdifferentialsplicingmultiplecomparisontimecoursedataimportatacseqepigeneticsregressionproprietaryplatformsgenesetenrichmentbatcheffectchipseq
7 stars 6.05 score 3 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.
infrastructureproprietaryplatformsexonarraymicroarrayonechannelguidataimportdatarepresentationpreprocessingqualitycontrolvisualizationreportwritingacghcopynumbervariantsdifferentialexpressiongeneexpressionsnptranscriptionaffymetrixanalysiscopy-numberdnaexpressionhpclarge-scalenotebookreproducibilityrna
10 stars 5.79 score 112 scripts 3 dependentsbioc
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
4.95 score 5 scripts 1 dependentsbioc
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.
statisticalmethoddifferentialmethylationgeneregulationgeneexpressionmethylationarraytranscriptionpreprocessingbatcheffectdataimportmrnamicroarraymicrornaarrayregressionclusteringrnaseqcopynumbervariationsequencingmicroarraynormalizationnetworkbayesianexonarrayonechanneltwochannelproprietaryplatformsalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentmultiplecomparisonqualitycontroltimecourse
4.88 score 15 scriptsbioc
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
4.60 score 3 scriptsbioc
SpatialOmicsOverlay:Spatial Overlay for Omic Data from Nanostring GeoMx Data
Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.
Maintained by Maddy Griswold. Last updated 5 months ago.
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsproprietaryplatformsrnaseqspatialdatarepresentationvisualizationopenjdk
4.30 score 8 scriptshenrikbengtsson
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.
proprietaryplatformsacghcopynumbervariantssnpmicroarrayonechanneltwochanneldataimportdatarepresentationpreprocessingqualitycontrol
1 stars 2.70 score 9 scriptsbioc
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.
microarraypreprocessingnormalizationgeneexpressionsurvivaltranscriptionsequencingtranscriptomicsbayesianclusteringregressionrnaseqmicrornaarraymrnamicroarrayfunctionalgenomicssystemsbiologyimmunooncologydifferentialexpressiongenesetenrichmentbatcheffectmultiplecomparisonqualitycontroltimecoursemetabolomicsproteomicsepigeneticscheminformaticsexonarrayonechanneltwochannelproprietaryplatformscellbiologybiomedicalinformaticsalternativesplicingdifferentialsplicingdataimportpathways
2.30 score