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chevron_left Gene expression clustering Background correction Bioinformatics workflows Normalization Batch effect correction Bioinformatics workflows chevron_right
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dChip specifications

Information


Unique identifier OMICS_00719
Name dChip
Alternative name DNA-Chip Analyzer
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Cheng Li <>

Additional information


https://sites.google.com/site/dchipsoft/tutorials-and-courses

Publication for DNA-Chip Analyzer

dChip in publications

 (6)
PMCID: 5512050
DOI: 10.1155/2017/1746426

[…] signal was taken as the measure of mrna abundance derived from the level of gene expression. microarray data were standardized using a z-score calculation. statistical analysis was performed by dchip software using anova filtering and followed by correction for multiple testing (estimation of expected false positives). hierarchical clustering was performed using the measure of euclidian […]

PMCID: 4094458
PMID: 24974883
DOI: 10.1186/1471-2148-14-147

[…] tissues), gse6901 (expression data for heat, cold and salt treatments), and gse14275 (expression data for heat-shock conditions) were used in an expression analysis of rice hsf genes. the program dchip version 2010 [] was used to perform the cluster analysis and to display the expression patterns of rice hsf genes based on the microarray data. gene-expression values were compared using […]

PMCID: 3935570
PMID: 24420575
DOI: 10.1093/jxb/ert471

[…] uk ltd., high wycombe, uk)] followed standard affymetrix protocols., data sets contained in the (.cel) files were normalized according to the robust multi-array average (rma) approach using dchip software (). further analysis was performed with the same software (; ). gene expression was considered as up- or down-regulated if the transcript level showed a minimum of a 1.3-fold change, […]

PMCID: 3464625
PMID: 22702538
DOI: 10.1186/1471-2164-13-241

[…] the copy number dosage at each snp of each individual. gmm models the signal intensity at each snp across the entire population (cohort) which differs from hmm approaches like cnat [], cnag [], dchip [], penncnv [] and quantisnp [] that model the signal sample by sample along each chromosome. other gmm implementations have been successfully used in the past for bac and cgh array analyses […]

PMCID: 3144989
PMID: 21743471
DOI: 10.1038/nn.2859

[…] were profiled per transgenic line, each representing a sample of ~1000 cells collected from a single litter. data was analyzed and cell-type-specific genes identified using resolver (rosetta) and dchip software. heatmaps were constructed by first filtering all probesets to remove those that did not show at least one 3-fold change between any pair of cell types, then standardizing […]


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dChip institution(s)
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
dChip funding source(s)
Supported by NIH grant 1R01GM077122

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