Chipster protocols

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Chipster specifications

Information


Unique identifier OMICS_00751
Name Chipster
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Version 3.12
Stability Stable
Maintained Yes

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  • person_outline Eija Korpelainen <>

Publication for Chipster

Chipster in pipelines

 (2)
2017
PMCID: 5613355
PMID: 28946896
DOI: 10.1186/s13072-017-0153-1

[…] and mapped to hg38 with bowtie [] within the chipster or galaxy platform [, ] retaining only uniquely mapped reads. peaks were called with macs [] using the broad option and using macs2 within the chipster platform. peak intersection was determined using bedtools []. density profiles of normalized reads per kilobase per million (rpkm) were generated in deeptools [] and visualized […]

2012
PMCID: 3597017
PMID: 23065637
DOI: 10.1242/dmm.010140

[…] profiles were determined using the illumina mousewg-6 v2.0 expression beadchip and genomestudio data analysis software (illumina, san diego, ca). gene expression analysis was performed with chipster v1.4.7 analysis software (csc, espoo, finland), and data normalization was carried out using the quantile method. quality control was performed to ensure the technical quality […]


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Chipster in publications

 (81)
PMCID: 5915154
PMID: 29707146
DOI: 10.18632/oncotarget.24880

[…] we performed microarray hybridizations to find clues on the possible mechanisms of action of aloe-emodin. ccrf-cem cells were treated with the ic50 of aloe-emodin or dmso for 48 h. using chipster software, 1712 genes were deregulated upon aloe-emodin treatment in comparison with dmso treatment as control. these genes were subsequently subjected to ingenuity pathway analysis (ipa) […]

PMCID: 5923468
PMID: 29614052
DOI: 10.3390/v10040174

[…] assembly pipeline [] and alignment using the computers at the centers for scientific computing []. the genome sequences were aligned using the multiple sequence alignment program mafft [] at the chipster platform []. the annotations were performed using rast server [] and manually annotated using the artemis genome browser and annotation tool []. some rast-identified open reading frames […]

PMCID: 5735295
PMID: 29270355
DOI: 10.1016/j.lrr.2017.12.001

[…] raw microarray data (affymetrix human genome u133 plus 2.0 array) were downloaded for the samples reported by gentles et al. (gse24006) and by novershtern et al., (gse24759) , imported into chipster (http://chipster.csc.fi/), normalized using robust multiarray average (rma) protocol and the expression of the ecm signature studied. to facilitate cross-comparison with gse24006, data […]

PMCID: 5879968
PMID: 29230965
DOI: 10.1002/jcsm.12265

[…] and quality control. raw data were normalized with quantile normalization (including log2‐transformation of the data), data quality was assessed, and statistical analyses were performed by using chipster software (it center for science, espoo, finland). statistically significant differences in individual genes between the groups were tested by using empirical bayes statistics […]

PMCID: 5722952
PMID: 29222481
DOI: 10.1038/s41598-017-17376-0

[…] gene chip scanner 3000 7g in biocenter oulu dna analysis core facility., affymetrix cel files (accession number gse83535, https://www.ncbi.nlm.nih.gov/geo/) were analyzed using dchip_2010_01 and chipster v3.4 (http://chipster.csc.fi/) softwares. array probe data were normalized to the mean expression level of each probe across the samples or data were normalized using the robust multiarray […]


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Chipster institution(s)
CSC - IT Center for Science, Keilaranta, Keilaniemi, Espoo, Finland; Finnish Red Cross Blood Service, Helsinki, Finland; Department of Pathology, VU University Medical Center, Amsterdam, Netherlands; Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Finland; FIMM Technology Centre, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland; Futurice, Helsinki, Finland
Chipster funding source(s)
Supported by a grant from Tekes - the Finnish Funding Agency for Technology and Innovation under the SYSBIO Research Programme; by the EMBRACE project grant which is funded by the European Commission within its FP6 Programme, under the thematic area “Life sciences, genomics and biotechnology for health”, contract number LUNG-CT-2004-512092.

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