:: DESCRIPTION
CNT-MD is a software for inferring the copy-number profiles of tumor clones and their evolution from fractional copy numbers obtained from multi-sample bulk sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael:
The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data.
RECOMB 2017: 318-335
:: DESCRIPTION
PCAdmix is a method that estimates local ancestry via principal components analysis (PCA) using phased haplotypes. The method considers data chromosome by chromosome.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hum Biol. 2012 Aug;84(4):343-64. doi: 10.3378/027.084.0401.
PCAdmix: principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations.
Brisbin A1, Bryc K, Byrnes J, Zakharia F, Omberg L, Degenhardt J, Reynolds A, Ostrer H, Mezey JG, Bustamante CD.
:: DESCRIPTION
DeMixT is a deconvolution framework for mixed transcriptomes from heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms.
::DEVELOPER
Statistical Bioinformatics Lab, The University of Texas M. D. Anderson Cancer Center
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wang Z, Cao S, Morris JS, Ahn J, Liu R, Tyekucheva S, Gao F, Li B, Lu W, Tang X, Wistuba II, Bowden M, Mucci L, Loda M, Parmigiani G, Holmes CC, Wang W.
Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration.
iScience. 2018 Nov 30;9:451-460. doi: 10.1016/j.isci.2018.10.028. Epub 2018 Nov 2. PMID: 30469014; PMCID: PMC6249353.
Bioinformatics. 2013 Aug 1;29(15):1865-71. doi: 10.1093/bioinformatics/btt301.
DeMix: deconvolution for mixed cancer transcriptomes using raw measured data.
Ahn J, Yuan Y, Parmigiani G, Suraokar MB, Diao L, Wistuba II, Wang W.
:: DESCRIPTION
CellR is a single cell-based data-driven method to recover and quantify the cellular composition of bulk transcriptional data. It is a fully unsupervised approach based on clustering the reference single-cell RNA-Seq (scRNA-seq) followed by extracting the unique marker genes defining each cell cluster.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Doostparast Torshizi A, Duan J, Wang K.
A computational tool for direct inference of cell-specific expression profiles and cellular composition from bulk-tissue RNA-seq in brain disorders.
bioRxiv, 2020.
:: DESCRIPTION
MS-Deconv is a combinatorial algorithm for spectral deconvolution. The algorithm first generates a large set of candidate isotopomer envelopes for a spectrum, then represents the spectrum as a graph, and finally selects its highest scoring subset of envelopes as a heaviest path in the graph.
::DEVELOPER
CCMS The Center for Computational Mass Spectrometry
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Cell Proteomics. 2010 Dec;9(12):2772-82. doi: 10.1074/mcp.M110.002766. Epub 2010 Sep 20.
Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach.
Liu X1, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner PA.
:: DESCRIPTION
DWLS (Dampened weighted least squares) is an estimation method for gene expression deconvolution, in which the cell-type composition of a bulk RNA-seq data set is computationally inferred.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Tsoucas D, Dong R, Chen H, Zhu Q, Guo G, Yuan GC.
Accurate estimation of cell-type composition from gene expression data.
Nature Communications. 10 (1), 2975 2019 Jul 5
:: DESCRIPTION
Huygens is high quality restoration (deconvolution) and visualization software for microscopists.
::DEVELOPER
Scientific Volume Imaging B.V.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
