Showing 7 of total 7 results (show query)
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.
acghcopynumbervariantssnpmicroarrayonechanneltwochannelgenetics
7 stars 7.63 score 34 scripts 9 dependentshenrikbengtsson
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 dependentshenrikbengtsson
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
1 stars 4.30 score 16 scripts 6 dependents
bioc
ADaCGH2:Analysis of big data from aCGH experiments using parallel computing and ff objects
Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.
Maintained by Ramon Diaz-Uriarte. Last updated 1 months ago.
3.48 score 3 scriptshenrikbengtsson
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
3.18 score 2 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 scriptshenrikbengtsson
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
1 stars 2.70 score 6 scripts