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Protocols

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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Maintainer


  • person_outline Eija Korpelainen

Publication for Chipster

Chipster citations

 (31)
library_books

Genomic Characterization of Sixteen Yersinia enterocolitica Infecting Podoviruses of Pig Origin

2018
Viruses
PMCID: 5923468
PMID: 29614052
DOI: 10.3390/v10040174

[…] novo 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 (ORFs […]

library_books

Prevention of chemotherapy‐induced cachexia by ACVR2B ligand blocking has different effects on heart and skeletal muscle

2017
PMCID: 5879968
PMID: 29230965
DOI: 10.1002/jcsm.12265

[…] ysis 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 and the Benjamin […]

library_books

Challenges in the Setup of Large scale Next Generation Sequencing Analysis Workflows

2017
Comput Struct Biotechnol J
PMCID: 5683667
PMID: 29158876
DOI: 10.1016/j.csbj.2017.10.001

[…] the-shelf pipeline solutions for commonly used analysis tasks, which can however be modified in a flexible and interactive way. Other publicly available analysis workflow systems include QuickNGS , , Chipster , ExScalibur , and many others (). Regarding the setup of the overall architecture, the daily operation and the choice of the particular tools, especially in customized pipelines, a user of a […]

call_split

Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state

2017
PMCID: 5613355
PMID: 28946896
DOI: 10.1186/s13072-017-0153-1
call_split See protocol

[…] 200 bps corresponding to mononucleosomes were isolated from gel and used for library generation. Around 35–60 million, 100-nt sequence reads were obtained 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 determi […]

call_split

Co infecting Reptarenaviruses Can Be Vertically Transmitted in Boa Constrictor

2017
PLoS Pathog
PMCID: 5289648
PMID: 28114434
DOI: 10.1371/journal.ppat.1006179
call_split See protocol

[…] tching the host genome and de novo sequence assembly were performed using MIRA version 4.0.2. (http://mira-assembler.sourceforge.net/) on CSC (IT Center for Science Ltd., Finland) Taito supercluster. Chipster v.3.1.0. was applied for the generation of subsets and any other handling of the data []. The reptarenavirus genomes de novo assembled from the parents’ samples were used to map the reads mat […]

call_split

Staphylococcus epidermidis Biofilm Released Cells Induce a Prompt and More Marked In vivo Inflammatory Type Response than Planktonic or Biofilm Cells

2016
Front Microbiol
PMCID: 5037199
PMID: 27729907
DOI: 10.3389/fmicb.2016.01530
call_split See protocol

[…] The arrays were analyzed using Chipster 2 (Kallio et al., ) with a custom cdf file in mogene21stmmentrezg.db, as available from Brainarray database (version 17; Sandberg and Larsson, ). Following Robust Multi-array Average normaliz […]


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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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