ABSOLUTE & HAPSEG
- Dchip Software Download Mac Software
- Dchip Software Download Mac Download
- Dchip Software Download Mac Os
- Dchip Software Download Mac Installer
Chip free download - SiS530 Single Chip VGA Graphics Driver (Windows 95/98), Realtek AC'97 Driver (Windows 98/Me/2000/XP/2003), Chip Set: ATI SMBus Driver Version A01, and many more programs. DNA-Chip Analyzer (dChip) is a software package implementing model-based expression analysis of oligonucleotide arrays and several high-level analysis procedures. The model-based approach allows probe-level analysis on multiple arrays. By pooling information across multiple arrays, it is possible to assess standard errors for the expression. CHIRP downloads¶ CHIRP is distributed as a series of automatically-generated builds. Any time we make a change to CHIRP, a build is created for it the next day. Thus, CHIRP is versioned by the date on which it was created, which makes it easy to determine if you have an older build.
Authors: Scott Carter et al. (Broad Institute)
What: 'When DNA is extracted from an admixed population of cancer andnormal cells, the information on absolute copy number per cancer cell islost in the mixing. The purpose of ABSOLUTE is to re-extract these datafrom the mixed DNA population. This process begins by generation ofsegmented copy number data, which is input to the ABSOLUTE algorithmtogether with pre-computed models of recurrent cancer karyotypes and,optionally, allelic fraction values for somatic point mutations. Theoutput of ABSOLUTE then provides re-extracted information on theabsolute cellular copy number of local DNA segments and, for pointmutations, the number of mutated alleles.'
Chip types: Affymetrix Mapping250K_Sty and GenomeWideSNP_6.
Operating system: R (access requires formal request)
URL: http://www.broadinstitute.org/cancer/cga/ABSOLUTE
What: 'When DNA is extracted from an admixed population of cancer andnormal cells, the information on absolute copy number per cancer cell islost in the mixing. The purpose of ABSOLUTE is to re-extract these datafrom the mixed DNA population. This process begins by generation ofsegmented copy number data, which is input to the ABSOLUTE algorithmtogether with pre-computed models of recurrent cancer karyotypes and,optionally, allelic fraction values for somatic point mutations. Theoutput of ABSOLUTE then provides re-extracted information on theabsolute cellular copy number of local DNA segments and, for pointmutations, the number of mutated alleles.'
Chip types: Affymetrix Mapping250K_Sty and GenomeWideSNP_6.
Operating system: R (access requires formal request)
URL: http://www.broadinstitute.org/cancer/cga/ABSOLUTE
We don't have any change log information yet for version 10.0.6 of Download Accelerator Plus. Sometimes publishers take a little while to make this information available, so please check back in a few days to see if it has been updated.
Affymetrix APT (Affymetrix Power Tools) software package
Dchip Software Download Mac Software
Authors: Affymetrix
What: A set of cross-Operating system command line programs thatimplement algorithms for analyzing and working with Affymetrix GeneChiparrays.
Chip types: Multiple chip types, not only SNP arrays.
Operating system: Linux, Mac OS X, Windows, Sun OS, ...
URL1:https://www.affymetrix.com/support/technical/product_updates/brlmm_algorithm.affx
URL2:http://www.affymetrix.com/support/developer/powertools/changelog/
See also: Affymetrix
BRLMM Analysis Tool (BAT) 2.0, which is a GUI for Windows.
What: A set of cross-Operating system command line programs thatimplement algorithms for analyzing and working with Affymetrix GeneChiparrays.
Chip types: Multiple chip types, not only SNP arrays.
Operating system: Linux, Mac OS X, Windows, Sun OS, ...
URL1:https://www.affymetrix.com/support/technical/product_updates/brlmm_algorithm.affx
URL2:http://www.affymetrix.com/support/developer/powertools/changelog/
See also: Affymetrix
BRLMM Analysis Tool (BAT) 2.0, which is a GUI for Windows.
Affymetrix Chromosome Analysis Suite (ChAS)
Authors: Affymetrix
What: 'Our entirely new Affymetrix Chromosome Analysis Suite (ChAS)software, designed specifically for cytogenetic researchers, gives youthe exact functions you need within an easy-to-use graphical interface.[...]'
Chip types: SNP and CN arrays.
Operating system: Windows (only?)
URL: http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?categoryIdClicked=&productId=131408
What: 'Our entirely new Affymetrix Chromosome Analysis Suite (ChAS)software, designed specifically for cytogenetic researchers, gives youthe exact functions you need within an easy-to-use graphical interface.[...]'
Chip types: SNP and CN arrays.
Operating system: Windows (only?)
URL: http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?categoryIdClicked=&productId=131408
Affymetrix CNAT v4.0
What: Copy-number analysis
Chip types: 10K, 100K, 500K.
Operating system: Windows, Unix
URL:http://www.affymetrix.com/support/developer/tools/devnettools.affx ('copynumber pipeline', command line)
URL:http://www.affymetrix.com/products/software/specific/cnat.affx (WindowsGUI)
References: Copy Number and Loss of Heterozygosity EstimationAlgorithms for the GeneChip Human Mapping Array Sets, Whitepaper,Affymetrix, 2006.
See also: H. Bengtsson, HB's Guide to CNATv4.0, 2007.
Chip types: 10K, 100K, 500K.
Operating system: Windows, Unix
URL:http://www.affymetrix.com/support/developer/tools/devnettools.affx ('copynumber pipeline', command line)
URL:http://www.affymetrix.com/products/software/specific/cnat.affx (WindowsGUI)
References: Copy Number and Loss of Heterozygosity EstimationAlgorithms for the GeneChip Human Mapping Array Sets, Whitepaper,Affymetrix, 2006.
See also: H. Bengtsson, HB's Guide to CNATv4.0, 2007.
Affymetrix GTC (Affymetrix Genotyping Console Software)
Authors: Affymetrix
What: Genotyping analysis software package designed to streamlinequality control, genotyping analysis, and copy-number analysis & LOH.No CN-analysis for GWS5. At least CN/LOH is hardwired to the defaultCDFs, that is, the 'full' CDFs wont do/make any difference (privatecommunication with Affymetrix, 2007-12-18).
Chip types: Mapping50K{Hind|Xba}240, Mapping250K{Nsp|Sty},GenomeWideSNP_5, GenomeWideSNP_6.
Operating system: Windows
URL:http://www.affymetrix.com/products_services/software/specific/genotyping_console_software.affx
What: Genotyping analysis software package designed to streamlinequality control, genotyping analysis, and copy-number analysis & LOH.No CN-analysis for GWS5. At least CN/LOH is hardwired to the defaultCDFs, that is, the 'full' CDFs wont do/make any difference (privatecommunication with Affymetrix, 2007-12-18).
Chip types: Mapping50K{Hind|Xba}240, Mapping250K{Nsp|Sty},GenomeWideSNP_5, GenomeWideSNP_6.
Operating system: Windows
URL:http://www.affymetrix.com/products_services/software/specific/genotyping_console_software.affx
Affymetrix IGB (Integrated Genome Browser)
Authors: Affymetrix
What: An open-source click'n'run Java genome browser.
Operating system: Java
URL:http://www.affymetrix.com/support/developer/tools/download_igb.affx
URL: http://genoviz.sourceforge.net/
What: An open-source click'n'run Java genome browser.
Operating system: Java
URL:http://www.affymetrix.com/support/developer/tools/download_igb.affx
URL: http://genoviz.sourceforge.net/
ArrayInitiative
What: 'A tool that simplifies creating custom Affymetrix CDFs'
Operating system: Any (Python)
URL: http://wellerlab.uncc.edu/ArrayInitiative/
Operating system: Any (Python)
URL: http://wellerlab.uncc.edu/ArrayInitiative/
ASCAT (Allele-Specific Copy number Analysis of Tumors) & ASPCF
Authors: P. van Loo, S. Nordgard et al.
What: 'Software for segmentation and allele-specific copy numberestimation for SNP array data.'
Chip types: SNP & CN microarrays.
Operating system: MATLAB and R. The bivariate segmentation method ASPCFis implemented in MATLAB and the ASCN estimation method ASCAT in R.
URL: http://heim.ifi.uio.no/bioinf/Projects/ASCAT/
What: 'Software for segmentation and allele-specific copy numberestimation for SNP array data.'
Chip types: SNP & CN microarrays.
Operating system: MATLAB and R. The bivariate segmentation method ASPCFis implemented in MATLAB and the ASCN estimation method ASCAT in R.
URL: http://heim.ifi.uio.no/bioinf/Projects/ASCAT/
AffyProbeMiner
Authors: Multiple - LMP, NCI, NIH, Georgetown University.
What: Generates Custom CDFs. A service to '1) generate a collectionof complete coding sequences composed of a) RefSeq records withaccessions starting with 'NM_' (e.g. NM_012345), b) validatedcomplete coding sequences in GenBank, and 2) regroup probes inAffymetrix chips into probe sets, where the probes in a probe set map toa consistent set of complete coding sequences [at the] gene-level[and/or] the transcript-level'.
Chip types: Several, but not all.
Operating system: Cross operating system (online)
URL: http://gauss.dbb.georgetown.edu/liblab/affyprobeminer/
What: Generates Custom CDFs. A service to '1) generate a collectionof complete coding sequences composed of a) RefSeq records withaccessions starting with 'NM_' (e.g. NM_012345), b) validatedcomplete coding sequences in GenBank, and 2) regroup probes inAffymetrix chips into probe sets, where the probes in a probe set map toa consistent set of complete coding sequences [at the] gene-level[and/or] the transcript-level'.
Chip types: Several, but not all.
Operating system: Cross operating system (online)
URL: http://gauss.dbb.georgetown.edu/liblab/affyprobeminer/
ArrayInitiative
Authors: C. Overall et al., University of North Carolina at Charlotte.
What: 'A Generic Tool for Creating Custom Affymetrix CDFs'.
Operating system: Python.
URL: http://wellerlab.uncc.edu/ArrayInitiative/
What: 'A Generic Tool for Creating Custom Affymetrix CDFs'.
Operating system: Python.
URL: http://wellerlab.uncc.edu/ArrayInitiative/
Bioconductor packages
Description: 'Available Bioconductor Software for ProcessingOligonucleotide Arrays'
URL: https://bioconductor.org//docs/workflows/oligoarrays/
URL: https://bioconductor.org//docs/workflows/oligoarrays/
Birdsuite
Description: 'The Birdsuite is a fully open-source set of tools todetect and report SNP genotypes, common Copy-Number Variants (CNVs), andrare/de novo CNVs in samples processed with the Affymetrix Operatingsystem. While most of the components of the suite can be runindividually (for instance, to simply do SNP genotyping), the Birdsuiteis especially intended for integrated analysis of SNPs and CNVs.'
Authors: Joshua Korn et al. (Broad Institute, MIT, ...)
Chip types: GenomeWideSNP_5 and GenomeWideSNP_6.
Operating system: Linux
URL: http://www.broad.mit.edu/mpg/birdsuite/
Authors: Joshua Korn et al. (Broad Institute, MIT, ...)
Chip types: GenomeWideSNP_5 and GenomeWideSNP_6.
Operating system: Linux
URL: http://www.broad.mit.edu/mpg/birdsuite/
CGB (The Cancer Genome Browser)
Description: 'The Cancer Genome Browser is a tool that allows thevisualization and analysis of high throughput data generated by largeinitiatives, such as the The Cancer Genome Atlas project.'
Authors:
Operating system: cross platform (MATLAB)
URL: http://code.google.com/p/cancergenome/
References:
Authors:
Operating system: cross platform (MATLAB)
URL: http://code.google.com/p/cancergenome/
References:
CisGenome
Description: 'An integrated tool for tiling array, ChIP-seq, genome andcis-regulatory element analysis.'
Authors:
Operating system: Windows, OS X and Linux.
URL: http://www.biostat.jhsph.edu/~hji/cisgenome/
Authors:
Operating system: Windows, OS X and Linux.
URL: http://www.biostat.jhsph.edu/~hji/cisgenome/
CMDS (Correlation Matrix Diagonal Segmentation)
Authors: Zhang et al.
What: A Fast Genome-wide Approach for Identifying Recurrent DNA CopyNumber Alterations across Cancer Patients.
Operating system: R (scripts; mail authors)
URL: https://dsgweb.wustl.edu/qunyuan/software/cmds/
References: Zhang, Q.; Ding, L.; Larson, D. E.; Koboldt, D. C.;McLellan, M. D.; Chen, K.; Shi, X.; Kraja, A.; Mardis, E. R.; Wilson, R.K.; Boreki, I. B. & Province, M. A. CMDS: a population-based method foridentifying recurrent DNA copy number aberrations in cancer fromhigh-resolution data. Bioinformatics, 2009.
Poster: Qunyuan Zhang, Li Ding, Aldi Kraja, Ingrid Boreki, Michael A.Province, Correlation Matrix Diagonal Segmentation (CMDS) - A FastGenome-wide Approach for Identifying Recurrent DNA Copy NumberAlterations across Cancer Patients, IGES (International GeneticEpidemiology Society), Sept. 2008, St. Louis, US.[ppt]
What: A Fast Genome-wide Approach for Identifying Recurrent DNA CopyNumber Alterations across Cancer Patients.
Operating system: R (scripts; mail authors)
URL: https://dsgweb.wustl.edu/qunyuan/software/cmds/
References: Zhang, Q.; Ding, L.; Larson, D. E.; Koboldt, D. C.;McLellan, M. D.; Chen, K.; Shi, X.; Kraja, A.; Mardis, E. R.; Wilson, R.K.; Boreki, I. B. & Province, M. A. CMDS: a population-based method foridentifying recurrent DNA copy number aberrations in cancer fromhigh-resolution data. Bioinformatics, 2009.
Poster: Qunyuan Zhang, Li Ding, Aldi Kraja, Ingrid Boreki, Michael A.Province, Correlation Matrix Diagonal Segmentation (CMDS) - A FastGenome-wide Approach for Identifying Recurrent DNA Copy NumberAlterations across Cancer Patients, IGES (International GeneticEpidemiology Society), Sept. 2008, St. Louis, US.[ppt]
CNAG
Authors: Seishi Ogawa Group, University of Tokyo
What: Copy-number analysis
Chip types: 100K, 500K.
Operating system: Windows
URL: http://www.genome.umin.jp/
References: CancerRes; 65(14), 6071-79 (2005).
See also: H. Bengtsson, HB's Guide to CNAG v2, 2007.
What: Copy-number analysis
Chip types: 100K, 500K.
Operating system: Windows
URL: http://www.genome.umin.jp/
References: CancerRes; 65(14), 6071-79 (2005).
See also: H. Bengtsson, HB's Guide to CNAG v2, 2007.
dChip (dChipSNP)
Authors: Cheng Li Group, DFCI and HSPH
What: Expression analysis, copy-number analysis, ...
Chip types: Several. For SNP & CN analysis: 10K, 100K, 500K, 5.0,6.0.
Operating system: Windows
URL: http://www.dchip.org/
References: (1) C. Li and W. Wong Model-based analysis ofoligonucleotide arrays: Expression index computation and outlierdetection, Proc. Natl. Acad. Sci, 2001, Vol. 98, 31-36. (2) M. Lin etal. dChipSNP: significance curve and clustering of SNP-array-basedloss-of-heterozygosity data, Bioinformatics, 2004, 20, 1233-40. (3) C.Li et al., Major copy proportion analysis of tumor samples using SNParrays. BMC Bioinformatics, 2008, 9:204.
See also: H. Bengtsson, HB's Guide todChip, 2005-2007.
Note: The dChipSNP (not dChip) executable is obsolete, cf. dChip thread'How to cite dChipetc?',Feb 16, 2010.
What: Expression analysis, copy-number analysis, ...
Chip types: Several. For SNP & CN analysis: 10K, 100K, 500K, 5.0,6.0.
Operating system: Windows
URL: http://www.dchip.org/
References: (1) C. Li and W. Wong Model-based analysis ofoligonucleotide arrays: Expression index computation and outlierdetection, Proc. Natl. Acad. Sci, 2001, Vol. 98, 31-36. (2) M. Lin etal. dChipSNP: significance curve and clustering of SNP-array-basedloss-of-heterozygosity data, Bioinformatics, 2004, 20, 1233-40. (3) C.Li et al., Major copy proportion analysis of tumor samples using SNParrays. BMC Bioinformatics, 2008, 9:204.
See also: H. Bengtsson, HB's Guide todChip, 2005-2007.
Note: The dChipSNP (not dChip) executable is obsolete, cf. dChip thread'How to cite dChipetc?',Feb 16, 2010.
EXALT (EXpression signature AnaLysis Tool)
Description: '...a resource for examining gene expression signatures inpublic domains. A gene expression signature in a microarray data set isdefined by EXALT as a list of significant genes with their groupcomparison codes and corresponding statistical scores. In essence, asignature represents a statistically validated fingerprint associatedwith a biological observation made from a gene expression experiment.EXALT has extracted signatures of differential genes within eachexperiment and built a large formatted collection of microarrayresults from NCBI GEO and published cancer studies. Thus, investigatorscan focus on discovery by searching, browsing, and querying onpre-computed gene expression signatures.'
References: J. Wu et al. Web-based interrogation of gene expressionsignatures using EXALT. BMC Bioinformatics, 2009
URL: http://seq.mc.vanderbilt.edu/exalt/
References: J. Wu et al. Web-based interrogation of gene expressionsignatures using EXALT. BMC Bioinformatics, 2009
URL: http://seq.mc.vanderbilt.edu/exalt/
Expander
Authors: Ron Shamir's Computational Genomics Laboratory, School ofComputer Science, Tel Aviv University
Operating system: Java
What: 'EXPANDER (EXpression Analyzer and DisplayER) is a java-based toolfor analysis of gene expression data. It is capable of (1) clustering(2) visualizing (3) biclustering and (4) performing downstream analysisof clusters and biclusters such as functional enrichment and promoteranalysis. In particular, it can analyze groups of genes for enrichmentof transcription factor binding sites in their promoters.'
URL: http://acgt.cs.tau.ac.il/expander/
Operating system: Java
What: 'EXPANDER (EXpression Analyzer and DisplayER) is a java-based toolfor analysis of gene expression data. It is capable of (1) clustering(2) visualizing (3) biclustering and (4) performing downstream analysisof clusters and biclusters such as functional enrichment and promoteranalysis. In particular, it can analyze groups of genes for enrichmentof transcription factor binding sites in their promoters.'
URL: http://acgt.cs.tau.ac.il/expander/
FARMS
Description: 'Factor Analysis for Robust Microarray Summarization(FARMS) is a model-based technique for summarizing high-densityoligonucleotide array data at probe level for Affymetrix GeneChips.'
Chip types: ?
Platform: R (Windows, Linux, ...?)
URL: http://www.bioinf.jku.at/software/farms/farms.html
References: Sepp Hochreiter, Djork-Arne Clevert & Klaus Obermayer, Anew summarization method for affymetrix probe leveldata,Bioinformatics 2006 22(8):943-949; [DOI:10.1093/bioinformatics/btl033].
Chip types: ?
Platform: R (Windows, Linux, ...?)
URL: http://www.bioinf.jku.at/software/farms/farms.html
References: Sepp Hochreiter, Djork-Arne Clevert & Klaus Obermayer, Anew summarization method for affymetrix probe leveldata,Bioinformatics 2006 22(8):943-949; [DOI:10.1093/bioinformatics/btl033].
GADA (Genome Alteration Detection Analysis)
Authors: Pique-Regi et al.
What: 'GADA is a fast and accurate method for detecting copy numberalterations (CNA) from array data. [...]'
Chip types: Generic segmentation method applicable to all raw CNs.
Operating system: ?
URL: https://groups.google.com//group/gadaproject
References: (1) Pique-Regi R and Gonzalez JR: 'R-Gada: a package forfast and parallel detection of copy number on multiple samples andvisualization', Bioinformatics , Submitted Dec 2008, (2) Pique-Regi R,Monso-Varona J,Ortega A, Seeger RC, Triche TJ, Asgharzadeh S: 'Sparserepresentation and Bayesian detection of the genome copy numberalterations from microarray data', Bioinformatics , Feb 2008 [PMID: 18203770]
What: 'GADA is a fast and accurate method for detecting copy numberalterations (CNA) from array data. [...]'
Chip types: Generic segmentation method applicable to all raw CNs.
Operating system: ?
URL: https://groups.google.com//group/gadaproject
References: (1) Pique-Regi R and Gonzalez JR: 'R-Gada: a package forfast and parallel detection of copy number on multiple samples andvisualization', Bioinformatics , Submitted Dec 2008, (2) Pique-Regi R,Monso-Varona J,Ortega A, Seeger RC, Triche TJ, Asgharzadeh S: 'Sparserepresentation and Bayesian detection of the genome copy numberalterations from microarray data', Bioinformatics , Feb 2008 [PMID: 18203770]
GEMCA
Authors: The Copy Number Variation Project, University of Tokyo
What: Detects copy number variants (CNVs).
Chip types: 500K
Operating system: Windows
URL:www.genome.rcast.u-tokyo.ac.jp/CNV/gemca_details.html
References: Komura et al., Genome-wide detection of human copy numbervariations using high density DNA oligonucleotide arrays, GenomeResearch 16, 1575-1584 (2006)
What: Detects copy number variants (CNVs).
Chip types: 500K
Operating system: Windows
URL:www.genome.rcast.u-tokyo.ac.jp/CNV/gemca_details.html
References: Komura et al., Genome-wide detection of human copy numbervariations using high density DNA oligonucleotide arrays, GenomeResearch 16, 1575-1584 (2006)
genoCN (genoCNA/genoCNV)
Authors: Sun et al.
What: Simultaneously dissect copy number states and genotypes using thedata from high density SNP arrays.
Chip types: 500K
Operating system: R
URL: http://www.bios.unc.edu/~wsun/software.htm
References: ??Sun et al., Integrated study of copy number states andgenotype calls using high-density SNP arrays. Nucleic Acids Res, 2009,37, 5365-5377.
What: Simultaneously dissect copy number states and genotypes using thedata from high density SNP arrays.
Chip types: 500K
Operating system: R
URL: http://www.bios.unc.edu/~wsun/software.htm
References: ??Sun et al., Integrated study of copy number states andgenotype calls using high-density SNP arrays. Nucleic Acids Res, 2009,37, 5365-5377.
GISTIC (Genomic Identification of Significant Targets in Cancer)
Authors: Beroukhim et al.
What: Finding common CN regions in tumors.Chip types: 100K. Possiblyothers as well.
Operating system: Linux 64-bit (binary only).
URL: http://www.broad.mit.edu/cancer/pub/GISTIC/
Manuals: GISTIC forGenePattern
References: Beroukhim et al. 2007, Assessing the significance ofchromosomal aberrations in cancer: Methodology and application toglioma,PNAS, December 2007.
What: Finding common CN regions in tumors.Chip types: 100K. Possiblyothers as well.
Operating system: Linux 64-bit (binary only).
URL: http://www.broad.mit.edu/cancer/pub/GISTIC/
Manuals: GISTIC forGenePattern
References: Beroukhim et al. 2007, Assessing the significance ofchromosomal aberrations in cancer: Methodology and application toglioma,PNAS, December 2007.
GTS (Genome Topography Scan)
Authors: Cameron Brennan
What:
Operating system: R (package also contains iCNA)
URL: http://cbio.mskcc.org/brennan/
Reference: Wiedemeyer R, Brennan C, Heffernan TP, Xiao Y, Mahoney J, etal. Feedback circuit among INK4 tumor suppressors constrains humanglioblastoma development. Cancer Cell, 2008, 13: 355-364.
What:
Operating system: R (package also contains iCNA)
URL: http://cbio.mskcc.org/brennan/
Reference: Wiedemeyer R, Brennan C, Heffernan TP, Xiao Y, Mahoney J, etal. Feedback circuit among INK4 tumor suppressors constrains humanglioblastoma development. Cancer Cell, 2008, 13: 355-364.
![Dchip Dchip](/uploads/1/1/8/2/118230688/277853324.gif)
iCNA (intragenic CNA)
Authors: Cameron Brennan
What: Identifying statistically significant intragenic CNA boundaries.
Operating system: R (in package GTS; see above)
URL: http://cbio.mskcc.org/brennan/
Reference:
What: Identifying statistically significant intragenic CNA boundaries.
Operating system: R (in package GTS; see above)
URL: http://cbio.mskcc.org/brennan/
Reference:
IdeogramBrowser
Author: Muller A et al.
What: 'A Java tool for visualization of genomic aberrations usingAffymetrix SNP arrays.'
Chip types: 10K, 100K, 500K, GWS5(?), GWS6(?), ...
Operating system: Java (cross OS)
URL: http://www.informatik.uni-ulm.de/ni/staff/HKestler/ideo/
References: Muller A et al., Visualization of genomic aberrations usingAffymetrix SNP arrays, Bioinformatics, 2007, 15;23(4):496-7 [PMID: 17138589]
What: 'A Java tool for visualization of genomic aberrations usingAffymetrix SNP arrays.'
Chip types: 10K, 100K, 500K, GWS5(?), GWS6(?), ...
Operating system: Java (cross OS)
URL: http://www.informatik.uni-ulm.de/ni/staff/HKestler/ideo/
References: Muller A et al., Visualization of genomic aberrations usingAffymetrix SNP arrays, Bioinformatics, 2007, 15;23(4):496-7 [PMID: 17138589]
IGV (Integrative Genomics Viewer)
Authors: ... (Broad Institute)
What: 'The Integrative Genomics Viewer (IGV) is a high-performancevisualization tool for interactive exploration of large, integrateddatasets.'. Can be linked to the TCGA data servers.
Operating system: Java (cross OS)
URL: http://www.broad.mit.edu/igv/
Documentation:http://www.broad.mit.edu/igv/doc/faq.html,http://www.broad.mit.edu/igv/doc/fileformats.html
References: ?
What: 'The Integrative Genomics Viewer (IGV) is a high-performancevisualization tool for interactive exploration of large, integrateddatasets.'. Can be linked to the TCGA data servers.
Operating system: Java (cross OS)
URL: http://www.broad.mit.edu/igv/
Documentation:http://www.broad.mit.edu/igv/doc/faq.html,http://www.broad.mit.edu/igv/doc/fileformats.html
References: ?
MADS+
Authors: Shen et al.
What: 'Discovery of differential splicing events from Affymetrix exonjunction array data.'
Requirements: R, RPy2, Python
References: Shen et al., MADS+: discovery of differential splicingevents from Affymetrix exon junction array data, Bioinformatics, 2009.
URL: http://www.medicine.uiowa.edu/Labs/Xing/MADSplus/
What: 'Discovery of differential splicing events from Affymetrix exonjunction array data.'
Requirements: R, RPy2, Python
References: Shen et al., MADS+: discovery of differential splicingevents from Affymetrix exon junction array data, Bioinformatics, 2009.
URL: http://www.medicine.uiowa.edu/Labs/Xing/MADSplus/
MAT (Model-based Analysis of Tiling arrays)
Authors: Johnson et al.
What: 'We propose a novel analysis algorithm MAT to reliably detectregions enriched by transcription factor Chromatin ImmunoPrecipitation(ChIP) on Affymetrix tiling arrays (chip).'
Operating system: Linux, source code
URL: http://liulab.dfci.harvard.edu/MAT/
References: (i) Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS,Brown M and Liu XS: Model-based analysis of tiling-arrays for ChIP-chip.Proc. Natl. Acad. Sci. USA 103 (2006) 12457-12462. (ii) Li W, CarrollJS, Brown M and Liu XS: xMAN: extreme MApping of OligoNucleotides.Accepted, BIOCOMP'07, BMC Genomics.
What: 'We propose a novel analysis algorithm MAT to reliably detectregions enriched by transcription factor Chromatin ImmunoPrecipitation(ChIP) on Affymetrix tiling arrays (chip).'
Operating system: Linux, source code
URL: http://liulab.dfci.harvard.edu/MAT/
References: (i) Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS,Brown M and Liu XS: Model-based analysis of tiling-arrays for ChIP-chip.Proc. Natl. Acad. Sci. USA 103 (2006) 12457-12462. (ii) Li W, CarrollJS, Brown M and Liu XS: xMAN: extreme MApping of OligoNucleotides.Accepted, BIOCOMP'07, BMC Genomics.
Microarray Blob Remover (MBR)
Authors: S. Liu et al.
What: 'We introduce a new software tool, the Microarray Blob Remover(MBR), which allows rapid visualization, detection, and removal of blobdefects of a variety of sizes and shapes from different types ofmicroarrays using their .CEL files. Removal of the affected probes inthe blob-defects using MBR was shown to significantly improvesensitivity and FDR compared to leaving the affected probes in theanalysis.'
Operating system: cross platform (Java)
URL: http://liulab.dfci.harvard.edu/Software/MBR/MBR.htm.html
What: 'We introduce a new software tool, the Microarray Blob Remover(MBR), which allows rapid visualization, detection, and removal of blobdefects of a variety of sizes and shapes from different types ofmicroarrays using their .CEL files. Removal of the affected probes inthe blob-defects using MBR was shown to significantly improvesensitivity and FDR compared to leaving the affected probes in theanalysis.'
Operating system: cross platform (Java)
URL: http://liulab.dfci.harvard.edu/Software/MBR/MBR.htm.html
OncoSNP
Authors: Christopher Yau
Operating system: MATLAB, Linux only
Licenses: For collaborators only
URL: https://sites.google.com/site/oncosnp/
References: ?
Operating system: MATLAB, Linux only
Licenses: For collaborators only
URL: https://sites.google.com/site/oncosnp/
References: ?
PennCNV
Authors: Wang et al.
What: Copy-number variant (CNV) analysis.
Chip types: Illumina, but also possible with Affymetrix GWS5 & GWS6.
Operating system: Linux, OS X, Windows. Languages: C and Perl.
URL: http://www.openbioinformatics.org/penncnv/
References: Wang K, Li M, Hadley D, Liu R, Glessner J, Grant S,Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov modeldesigned for high-resolution copy number variation detection inwhole-genome SNP genotyping data. Genome Research 17:1665-1674, 2007.
What: Copy-number variant (CNV) analysis.
Chip types: Illumina, but also possible with Affymetrix GWS5 & GWS6.
Operating system: Linux, OS X, Windows. Languages: C and Perl.
URL: http://www.openbioinformatics.org/penncnv/
References: Wang K, Li M, Hadley D, Liu R, Glessner J, Grant S,Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov modeldesigned for high-resolution copy number variation detection inwhole-genome SNP genotyping data. Genome Research 17:1665-1674, 2007.
PerfectMatch
What: Position-Dependent-Nearest-Neighbor (PDNN) Model by the originalauthors - 'A PC program for Affymetrix microarray data analysis usingPDNN model'.
Operating system: Windows.
URL:http://odin.mdacc.tmc.edu/~zhangli/PerfectMatch/
References: Zhang L, Miles, MF, and Aldape KD. A model of molecularinteractions on short oligonucleotide microarrays. NatureBiotechnology, 2003, 21, 818-821.
Operating system: Windows.
URL:http://odin.mdacc.tmc.edu/~zhangli/PerfectMatch/
References: Zhang L, Miles, MF, and Aldape KD. A model of molecularinteractions on short oligonucleotide microarrays. NatureBiotechnology, 2003, 21, 818-821.
PhyloTrac
What: 'PhyloTrac is an application for the visualization and analysis ofPhyloChip microarrays. The PhyloChip is a popular 16S rRNA genemicroarray for microbial surveys, and has been successfully used tostudy the microbial diversity of several interesting environments.'
Operating system: Mac OS X, Linux, and Windows.
URL: http://www.phylotrac.org/
Authors: J. Ravel et al.
References:
Operating system: Mac OS X, Linux, and Windows.
URL: http://www.phylotrac.org/
Authors: J. Ravel et al.
References:
PICNIC (Predicting Integral Copy Numbers In Cancer)
Authors: Greenman, C.D et al.
What: '[...] includes improved normalisation of the data together withdetermination of underlying copy number for each segment by genome wideanalysis of allele ratio and signal strength data. The data issubsequently rescaled and plotted onto its predicted underlying integervalue and segmentation applied (it should be noted that rescaling theraw data to the underlying absolute copy number can affect the spread ofthe data points).'
Chip types: GenomeWideSNP_6
Operating system: MATLAB
URL: http://www.sanger.ac.uk/genetics/CGP/Software/PICNIC/
URL 2:http://www.sanger.ac.uk/genetics/CGP/CopyNumberMapping/Affy_SNP6.shtml
References: Greenman, C.D et al. (submitted)
What: '[...] includes improved normalisation of the data together withdetermination of underlying copy number for each segment by genome wideanalysis of allele ratio and signal strength data. The data issubsequently rescaled and plotted onto its predicted underlying integervalue and segmentation applied (it should be noted that rescaling theraw data to the underlying absolute copy number can affect the spread ofthe data points).'
Chip types: GenomeWideSNP_6
Operating system: MATLAB
URL: http://www.sanger.ac.uk/genetics/CGP/Software/PICNIC/
URL 2:http://www.sanger.ac.uk/genetics/CGP/CopyNumberMapping/Affy_SNP6.shtml
References: Greenman, C.D et al. (submitted)
PLASQ, PLASQ10K, PLASQ500K
Authors: LaFramboise T et al., Department of MedicalOncology,Dana-Farber Cancer Institute.
What: Genotyping, copy-number analysis.
Chip types: 10K, 100K, 500K.
Operating system: R
URL: http://mendel.cwru.edu/laframboiselab/software.php
References: LaFramboise T, Harrington D, Weir BA. PLASQ: a generalizedlinear model-based procedure to determine allelic dosage in cancer cellsfrom SNP array data. Biostatistics. April 2007, 8(2):323-36.
What: Genotyping, copy-number analysis.
Chip types: 10K, 100K, 500K.
Operating system: R
URL: http://mendel.cwru.edu/laframboiselab/software.php
References: LaFramboise T, Harrington D, Weir BA. PLASQ: a generalizedlinear model-based procedure to determine allelic dosage in cancer cellsfrom SNP array data. Biostatistics. April 2007, 8(2):323-36.
ProbeMapper
Authors: JD Allen et al., Quantitative Biomedical Research Initiative,Southwestern Medical Center.
What: 'This software allows users to find associations between EntrezGene IDs and microarray probe IDs for eight major gene expressionplatforms.'
Operating system: Online service as well as R package
URL: http://qbrc.swmed.edu/software/probemapper-live/
URL: https://cran.r-project.org//web/packages/probemapper/
What: 'This software allows users to find associations between EntrezGene IDs and microarray probe IDs for eight major gene expressionplatforms.'
Operating system: Online service as well as R package
URL: http://qbrc.swmed.edu/software/probemapper-live/
URL: https://cran.r-project.org//web/packages/probemapper/
PuMaQC (Public Microarray Data Quality Control)
Authors: JP. Corte-Real and PV. Nazarov
What: 'A robust, easy to use, all-in-one pipeline for public microarraydata handling based on 3 sequential steps: i) search for raw Affymetrixdata in GEO; ii) import and preprocessing of CEL files; iii) QC/QA withidentification and removal of low quality arrays.'
Operating system: Any that runs Affymetrix Power Tools and R.
URL: http://sablab.net/PuMaQC/
What: 'A robust, easy to use, all-in-one pipeline for public microarraydata handling based on 3 sequential steps: i) search for raw Affymetrixdata in GEO; ii) import and preprocessing of CEL files; iii) QC/QA withidentification and removal of low quality arrays.'
Operating system: Any that runs Affymetrix Power Tools and R.
URL: http://sablab.net/PuMaQC/
QuantiSNP
Authors: Wang et al.
What: Copy-number variant (CNV) analysis.
Chip types: Illumina, but QuantiSNP v1.1 supports Affymetrix as well.
Operating system: Linux (32-bit & 64-bit), ...???
URL: http://www.well.ox.ac.uk/QuantiSNP/.
Forum: http://groups.google.co.uk/group/quantisnp
References: Colella S. et al. QuantiSNP: an Objective BayesHidden-Markov Model to detect and accurately map copy number variationusing SNP genotyping data. Nucleic Acids Res, 2007, 35, 2013-2025.
What: Copy-number variant (CNV) analysis.
Chip types: Illumina, but QuantiSNP v1.1 supports Affymetrix as well.
Operating system: Linux (32-bit & 64-bit), ...???
URL: http://www.well.ox.ac.uk/QuantiSNP/.
Forum: http://groups.google.co.uk/group/quantisnp
References: Colella S. et al. QuantiSNP: an Objective BayesHidden-Markov Model to detect and accurately map copy number variationusing SNP genotyping data. Nucleic Acids Res, 2007, 35, 2013-2025.
RAE
What: For paired tumor-normal log2 CN ratios...
Chip types: Affymetrix, Illumina, ... (any total CN platform for whichone can run CBS)
Operating system: R (a set of R and shell scripts; not packaged)
URL: http://cbio.mskcc.org/downloads/rae/
Reference: Taylor BS, Barretina J, Socci ND, DeCarolis P, Ladanyi M,Meyerson M, Singer S, Sander C. Functional copy-number alterations incancer. PLoS ONE. 2008 Sep 11;3(9):e3179.
Chip types: Affymetrix, Illumina, ... (any total CN platform for whichone can run CBS)
Operating system: R (a set of R and shell scripts; not packaged)
URL: http://cbio.mskcc.org/downloads/rae/
Reference: Taylor BS, Barretina J, Socci ND, DeCarolis P, Ladanyi M,Meyerson M, Singer S, Sander C. Functional copy-number alterations incancer. PLoS ONE. 2008 Sep 11;3(9):e3179.
rMAT
What: 'rMAT is an open-source R package based on the popular MATsoftware for the normalization, detection and quantification ofChIP-enriched regions. rMAT has been written from scratch in C and R andprovides an efficient implementation of the functionality of MAT as wellnovel statistical normalization techniques not available in the originalMAT. [...]
Operation systems: R
URL: http://wiki.rglab.org/index.php?title=Public:RMAT
References: (1) A. Droit, C. Cheung, and R. Gottardo (2010). rMAT - anR/Bioconductor package for analyzing ChIP-chipexperiments,Bioinformatics, 26:678-679. (2) W. E. Johnson, Li, W.,Meyer, C. A., Gottardo, R., Carroll, J. S., Brown, M., and Liu, X. S.(2006). Model-based analysis of tiling-arrays forChIP-chip. PNAS 103:12457-12462.
Operation systems: R
URL: http://wiki.rglab.org/index.php?title=Public:RMAT
References: (1) A. Droit, C. Cheung, and R. Gottardo (2010). rMAT - anR/Bioconductor package for analyzing ChIP-chipexperiments,Bioinformatics, 26:678-679. (2) W. E. Johnson, Li, W.,Meyer, C. A., Gottardo, R., Carroll, J. S., Brown, M., and Liu, X. S.(2006). Model-based analysis of tiling-arrays forChIP-chip. PNAS 103:12457-12462.
SEURAT
Authors: Gribov A et al.
What: SEURAT is a software tool which provides interactive visualizationcapability for the integrated analysis of high-dimensional geneexpression data. Gene expression data can be analyzed together withassociated clinical data, array CGH (comparative genomic hybridization),SNP array (single nucleotide polymorphism) data and available geneannotations in an integrated manner. The different data types areorganized by a comprehensive data manager.
URL: http://seurat.r-forge.r-project.org/
References: Gribov A et al. SEURAT: visual analytics for the integratedanalysis of microarray data. BMC Med Genomics, , 2010.
Operating system: R+Java
What: SEURAT is a software tool which provides interactive visualizationcapability for the integrated analysis of high-dimensional geneexpression data. Gene expression data can be analyzed together withassociated clinical data, array CGH (comparative genomic hybridization),SNP array (single nucleotide polymorphism) data and available geneannotations in an integrated manner. The different data types areorganized by a comprehensive data manager.
URL: http://seurat.r-forge.r-project.org/
References: Gribov A et al. SEURAT: visual analytics for the integratedanalysis of microarray data. BMC Med Genomics, , 2010.
Operating system: R+Java
SNPMaP
Dchip Software Download Mac Download
Authors: Davis et al.
What: 'The SNPMaP package for R provides a framework for the analysisof SNPMaP (SNP microarrays and pooling) genome-wide association datausing the tools available in the increasingly popular Open Sourcestatistical computing environment.'
Chip types: Mapping250K_{Nsp|Sty}, GenomeWideSNP_5,GenomeWideSNP_6.
Operating system: R
URL: http://sgdp.iop.kcl.ac.uk/snpmap/
References: Davis, O.S.P., Plomin, R., & Schalkwyk, L.C. (submitted forpublication). The SNPMaP package for R: A framework for genome-wideassociation using DNA pooling on microarrays, 2008.
What: 'The SNPMaP package for R provides a framework for the analysisof SNPMaP (SNP microarrays and pooling) genome-wide association datausing the tools available in the increasingly popular Open Sourcestatistical computing environment.'
Chip types: Mapping250K_{Nsp|Sty}, GenomeWideSNP_5,GenomeWideSNP_6.
Operating system: R
URL: http://sgdp.iop.kcl.ac.uk/snpmap/
References: Davis, O.S.P., Plomin, R., & Schalkwyk, L.C. (submitted forpublication). The SNPMaP package for R: A framework for genome-wideassociation using DNA pooling on microarrays, 2008.
SOMATICs
Authors: Davis et al.
What: ...
Chip types: Illumina.
Operating system: R
URL: http://www.lerner.ccf.org/gmi/igac/SOMsuppScriptR080412.txt (ascript)
References: Assié, G.; LaFramboise, T.; Platzer, P.; Bertherat, J.;Stratakis, C. A. & Eng, C. SNP arrays in heterogeneous tissue: highlyaccurate collection of both germline and somatic genetic informationfrom unpaired single tumor samples. Am J Hum Genet, 2008.
What: ...
Chip types: Illumina.
Operating system: R
URL: http://www.lerner.ccf.org/gmi/igac/SOMsuppScriptR080412.txt (ascript)
References: Assié, G.; LaFramboise, T.; Platzer, P.; Bertherat, J.;Stratakis, C. A. & Eng, C. SNP arrays in heterogeneous tissue: highlyaccurate collection of both germline and somatic genetic informationfrom unpaired single tumor samples. Am J Hum Genet, 2008.
Tumor Aberration Prediction Suite (TAPS)
Authors: M. Rasmussen et al.
Operating system: R
URL: http://array.medsci.uu.se/taps/
Operating system: R
URL: http://array.medsci.uu.se/taps/
TuMult
What: 'TuMult was developed for the analysis of several tumors from thesame patient. Using the chromosome breakpoints these tumors have incommon, TuMult reconstructs the tumor lineage and the sequence ofchromosome aberrations occurring during tumorigenesis. TuMult may beapplied to any kind of copy number data.'
Chip types: Affymetrix, Illumina
Operating system: R
URL:http://bioserv.rpbs.univ-paris-diderot.fr/~letouze/TuMult/ALGORITHM.html
References: Letouzé, E.; Allory, Y.; Bollet, M. A.; Radvanyi, F. &Guyon, F. Analysis of the copy number profiles of several tumor samplesfrom the same patient reveals the successive steps in tumorigenesis.Genome Biol, 2010.
Chip types: Affymetrix, Illumina
Operating system: R
URL:http://bioserv.rpbs.univ-paris-diderot.fr/~letouze/TuMult/ALGORITHM.html
References: Letouzé, E.; Allory, Y.; Bollet, M. A.; Radvanyi, F. &Guyon, F. Analysis of the copy number profiles of several tumor samplesfrom the same patient reveals the successive steps in tumorigenesis.Genome Biol, 2010.
VanillaICE
Author: Robert Scharpf et al.
What: 'Hidden Markov model for identifying chromosomal alterations inhigh-throughput SNP arrays.'
Chip types: Affymetrix, ...
URL: https://www.bioconductor.org//packages/release/bioc/html/VanillaICE.html
What: 'Hidden Markov model for identifying chromosomal alterations inhigh-throughput SNP arrays.'
Chip types: Affymetrix, ...
URL: https://www.bioconductor.org//packages/release/bioc/html/VanillaICE.html
Dchip Software Download Mac Os
X:MAP
Description: Exon array analysis.
Chip types: Human, Mouse, and Rat Exon 1.0 ST.
Operating system: Has an R interface.
References: [1] Yates T, Okoniewski MJ, and Miller CJ. X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis, Nucleic Acids Research, 2007. [2] Okoniewski MJ, Yates T, Dibben S, and Miller CJ, An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data, Genome Biology 2007.
URL: http://xmap.picr.man.ac.uk/
Chip types: Human, Mouse, and Rat Exon 1.0 ST.
Operating system: Has an R interface.
References: [1] Yates T, Okoniewski MJ, and Miller CJ. X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis, Nucleic Acids Research, 2007. [2] Okoniewski MJ, Yates T, Dibben S, and Miller CJ, An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data, Genome Biology 2007.
URL: http://xmap.picr.man.ac.uk/
Affymetrix Fusion Software Developers Kit (SDK)
Author: Affymetrix Inc.
What: A file parser library written C++ and Java that can read most ofAffymetrix Data FileFormats,e.g. CDF, CEL, CHP, and BPMAP.
URL: http://www.affymetrix.com/support/developer/fusion/
Author: Affymetrix Inc.
What: A file parser library written C++ and Java that can read most ofAffymetrix Data FileFormats,e.g. CDF, CEL, CHP, and BPMAP.
URL: http://www.affymetrix.com/support/developer/fusion/
Affymetrix CEL File Conversion Tool
Author: Affymetrix Inc.
What: The cell intensity file (CEL) File Conversion Tool converts allAffymetrix CEL files in a specified directory from version 3 format(ASCII - MAS 5 compatible format) to and from version 4 format (binary -GCOS compatible format).
What: The cell intensity file (CEL) File Conversion Tool converts allAffymetrix CEL files in a specified directory from version 3 format(ASCII - MAS 5 compatible format) to and from version 4 format (binary -GCOS compatible format).
URL: http://www.affymetrix.com/support/developer/tools/devnettools.affx
Affymetrix CDF File Conversion Tool
Author: Affymetrix Inc.
What: The chip definition file (CDF) File Conversion Tool will convertall Affymetrix CDF files (GCOS library files) in a specified directoryfrom its current ASCII format to a new binary format that will be usedin future versions of the GCOS software. DO NOT use this tool to convertlibrary files managed by the GCOS 1.1 or below software as that softwaredoes not understand the new binary format.
URL:http://www.affymetrix.com/support/developer/tools/devnettools.affx
What: The chip definition file (CDF) File Conversion Tool will convertall Affymetrix CDF files (GCOS library files) in a specified directoryfrom its current ASCII format to a new binary format that will be usedin future versions of the GCOS software. DO NOT use this tool to convertlibrary files managed by the GCOS 1.1 or below software as that softwaredoes not understand the new binary format.
URL:http://www.affymetrix.com/support/developer/tools/devnettools.affx
AssociationViewer
What: 'A Java application used in whole genome analysis to display SNPsin a genomic context. Supplementary data is downloaded from variouspublic data sources on the fly and saved locally in a cache. Custom datacan be added as supplementary tracks. '
Operating system: Java (cross Operating system)
Author: Armand Valsesia and Olivier Martin
URL: http://sourceforge.net/projects/associationview/
Operating system: Java (cross Operating system)
Author: Armand Valsesia and Olivier Martin
URL: http://sourceforge.net/projects/associationview/
CELUtil
Author: D. Paladini et al., 2005.
URL: http://www.bioinformatics.org/celutil/
Genome Environment Browser (GEB)
Operating system: Java (cross Operating system)Reference: Huntley D etal., Genome Environment Browser (GEB): a dynamic browser for visualisinghigh-throughput experimental data in the context of genome features, BMCBioinformatics, Nov 2008, 9:501, DOI:10.1186/1471-2105-9-501.URL:http://web.bioinformatics.ic.ac.uk/geb/
URL: http://www.bioinformatics.org/celutil/
Genome Environment Browser (GEB)
Operating system: Java (cross Operating system)Reference: Huntley D etal., Genome Environment Browser (GEB): a dynamic browser for visualisinghigh-throughput experimental data in the context of genome features, BMCBioinformatics, Nov 2008, 9:501, DOI:10.1186/1471-2105-9-501.URL:http://web.bioinformatics.ic.ac.uk/geb/
GoldSurfer2
Authors:
What: 'A comprehensive tool for the analysis and visualization of wholegenome association studies'
Chip types: Non-specific, i.e. imports genotyping data in some standardfile formats.
Operating system: Java (cross Operating system)
URL:http://www.well.ox.ac.uk/~fredrikp/gs2.html
References: Pettersson, F., Jonsson, O. and Cardon, L.R., GOLDsurfer:three dimensional display of linkage disequilibrium. Bioinformatics.2004;20(17):3241-3.
What: 'A comprehensive tool for the analysis and visualization of wholegenome association studies'
Chip types: Non-specific, i.e. imports genotyping data in some standardfile formats.
Operating system: Java (cross Operating system)
URL:http://www.well.ox.ac.uk/~fredrikp/gs2.html
References: Pettersson, F., Jonsson, O. and Cardon, L.R., GOLDsurfer:three dimensional display of linkage disequilibrium. Bioinformatics.2004;20(17):3241-3.
Ultrasome
Dchip Software Download Mac Installer
Authors: Bjorn Nilsson et al. (Broad etc).What: 'Ultrasome is anefficient methodology for detecting and delineating gains and losses ofchromosomal material in DNA copy-number data.'
References: Bjorn Nilsson; Mikael Johansson; Fatima Al-Shahrour; AnneE. Carpenter; and Benjamin L. Ebert. 'Ultrasome: efficient aberrationcaller for copy number studies of ultra-high resolution'. Bioinformatics(2009); DOI: 10.1093/bioinformatics/btp091
URL http://www.broad.mit.edu/ultrasome/
References: Bjorn Nilsson; Mikael Johansson; Fatima Al-Shahrour; AnneE. Carpenter; and Benjamin L. Ebert. 'Ultrasome: efficient aberrationcaller for copy number studies of ultra-high resolution'. Bioinformatics(2009); DOI: 10.1093/bioinformatics/btp091
URL http://www.broad.mit.edu/ultrasome/
![Dchip Software Download Mac Dchip Software Download Mac](/uploads/1/1/8/2/118230688/346863866.png)
MS-DOS subst
What: The [Windows/MS-DOS] console'subst' utility makes a driveletter to any Windows directory, e.g. subst Y: 'C:/Documents andSettings/JohnDoe/Documents/MyResearch/Projects/aroma.affymetrix/ProjectA/'. This provides aworkaround when a pathname becomes too long for Windows. The maximumnumber of symbols in a pathname is 256, including file separators '/' or', but excluding the drive letter, and initial file separator (e.g.'C:/'), and the string terminator ('0'), cf. MSDN - Naming a File orDirectory. In Rv2.8.x, the limit is one symbol less, i.e. 255.
Operating system: Windows
URL: http://en.wikipedia.org/wiki/Subst
Operating system: Windows
URL: http://en.wikipedia.org/wiki/Subst