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on page 1 showing 6 out of 6 results

Cite this (AbsCN-seq, RRID:SCR_006409)

URL: http://bioinformatics.oxfordjournals.org/content/early/2014/01/02/bioinformatics.btt759.abstract?sid=e62f3c2b-26dc-428b-ba24-99e92a277d77

Resource Type: Resource, software resource

Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.

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    GSE1456

Cite this (GSE1456, RRID:SCR_003642)

URL: http://ranchobiosciences.com/gse1456/

Resource Type: Resource, data set, data or information resource

Curated series of expression data for 159 tumors from which RNA could be collected in sufficient amounts and quality for analysis from breast cancer patients. Tissue material was collected from all breast cancer patients receiving surgery at Karolinska Hospital from 1994-1996.

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    GSE4922

Cite this (GSE4922, RRID:SCR_003557)

URL: http://ranchobiosciences.com/gse4922/

Resource Type: Resource, data set, data or information resource

Curated data set of a study that investigated the expression profiles of 347 primary invasive breast tumors on Affymetrix microarrays. Three separate breast cancer cohorts were analyzed: 1) Uppsala (n=249), 2) Stockholm (n=58), 3) Singapore (n=40). The Uppsala and Singapore data can be accessed in GSE4922. The Stockholm cohort data can be accessed at GEO Series GSE1456.

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    HPA

Cite this (HPA, RRID:SCR_006710)

URL: http://www.proteinatlas.org/

Resource Type: Resource, database, biospecimen repository, service resource, storage service resource, atlas, material storage repository, data or information resource

Public database with millions of high-resolution images showing the spatial distribution of proteins in different normal human tissues and cancer types, as well as different human cell lines. The data is released together with application-specific validation performed for each antibody, including immunohistochemisty, Western blot analysis and, for a large fraction, a protein array assay and immunofluorescent based confocal microscopy. The database has been developed in a gene-centric manner with the inclusion of all human genes predicted from genome efforts. Search functionalities allow for complex queries regarding protein expression profiles, protein classes and chromosome location. Antibodies included have been analyzed using a standardized protocol in a single attempt without further efforts to optimize the procedure and therefore it cannot be excluded that certain observed binding properties are due to technical rather than biological reasons and that further optimization could result in a different outcome. Submission of antibodies: The Swedish Human Proteome Atlas (HPA) program, invites submission of antibodies from both academic and commercial sources to be included in the human protein atlas. All antibodies will be validated by the HPA-program by a standard procedure and antibodies that are accepted will be use in the tissue- profiling program to generate high-resolution immunohistochemistry images representing a wide spectrum of normal tissues and cancer types.

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Cite this (Mutascope, RRID:SCR_001265)

URL: http://sourceforge.net/projects/mutascope/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.

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Cite this (Patchwork, RRID:SCR_000072)

URL: http://patchwork.r-forge.r-project.org/

Resource Type: Resource, software resource

Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data.

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