AnnotatedBCGEData - 100+ Curated Breast Cancer Gene Expression Data sets
AnnotatedBCGEData is an R Bioconductor package that provides access to more than 100 gene-expression datasets generated using microarray and RNA- sequencing technologies. We collected these datsets from public repositories, including Gene Expression Omnibus, ArrayExpress, and The Cancer Genome Atlas. Where feasible, we obtained and reprocessed the raw data using computational pipelines and annotations that were standardized and more updated than those used to process the data originally. Additionally, we annotated the sample metadata using oncology terms from the National Cancer Institute Thesaurus. This was necessary because different data submitters used different terminology to describe breast-cancer patients and samples. Mapping the metadata to ontology terms makes it possible for users to search the data using these standardized terms.
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experimentdatacancerdataexpressiondatahomo_sapiens_datageoarrayexpresstissuemicroarraydatasequencingdatabreastcancerdatagenometissuemicroarraydatadatapkg
5.08 score 1 stars 4 scriptsSCAN.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.
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immunooncologysoftwaremicroarraypreprocessingrnaseqtwochannelonechannel
3.73 score 27 scripts 678 downloads