User: kmezhoud

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kmezhoud0
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Tunisia
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Posts by kmezhoud

<prev • 15 results • page 1 of 2 • next >
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commit changes with scenario 1
... Dear All, I am trying to commit some changes to bioCancer. the issue is no changes added to commit. Please, here is commands. Thanks  git clone https://github.com/Bioconductor-mirror/bioCancer cd bioCancer/ ../update_remotes.sh Already on 'master' Your branch is up-to-date with 'origin/mas ...
svn git mirror scenario 1 written 16 months ago by kmezhoud0
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built vignette using knitr
... Dear All, I am setting vignette using knitr package. In DESCRIPTION file I added: Suggests:     BiocStyle,     rmarkdown (>= 0.4.2),     testthat (>= 0.10.0),     rappdirs VignetteBuilder: knitr In Rmd file, I started by: --- title: "bioCancer: Interactive Multi-OMICS Cancers Data Visuali ...
bioccheck knitr vignettes built no-ascii written 19 months ago by kmezhoud0
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Answer: A: manage github dependency , not CRAN nor bioc
... Thanks, Ok for bioc-devel list. Just for to close. https://cran.r-project.org/web/packages/devtools/vignettes/dependencies.html   Thanks ...
written 22 months ago by kmezhoud0
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manage github dependency , not CRAN nor bioc
... Dear bioC, How can I use a github (not CRAN) dependency in bioconductor package? I added in DESCRIPTION Remotes: github::vnijs/MathJaxR (>= 0.11)   but does not work. Karim Thanks ...
github dependency written 22 months ago by kmezhoud0
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Answer: A: detect cancer in some tissue
... Hi, Sorry for the delay. There is no statistic stage in any genomics data, to predict  if cancer is being or not. If you would like to compare your data with existing data, you need to clean up the raw data generated by affimetrix. I think there are some packages that do these. I didn't use it. I ...
written 22 months ago by kmezhoud0
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Answer: A: Reactome pathway analysis using ReactomePA
... Hi, You can just add this line  GeneID<- unname(unlist(translate(GeneList, org.Hs.egSYMBOL2EG))) Karim ...
written 2.1 years ago by kmezhoud0
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PSICQUIC: Direction of interaction
... Hi, PSICQUIC is an interesting package. it groups multiple interactomics databases. Specially reactomeFIs provider displays the DIRECTION of the interaction in column 4 (see sample below).  I am seeking for this kind of information. If PSICQUIC does not have this kind of information, is there an ...
network protein interaction analysis written 2.4 years ago by kmezhoud0
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Circos Styling plots is now easy with canceR package
... Hi, Circular layout is an interesting way to integrate multi-omics heterogeneous  and big data of cancer disease in the same plot. The goal is to make easy the interpretation and the exploring of the relationships between cancers, genes or dimensions.  There are two R packages (RCircos and Circlize ...
visualization cancer omiccircos written 2.5 years ago by kmezhoud0
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Answer: A: CanceR: Survival plots
... Dear All,  Survival Plots  In medical research is often useful to estimate the survival of patient amount time at tumor stage, or after treatment or particular event. The OS MONTHS is the overall Survival duration of patient after the first surgery. The OS STATUS is the event at OS MONTHS. The survi ...
written 2.6 years ago by kmezhoud0
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CanceR: Survival plots
... Hi, Thanks it is interesting to add Survival plots The phenoTest menu may has in part what do you expect (without curve).  It is possible to cluster a list of genes significantly regulated (gene expression) at a range of tumor size (continuous variable) or tumoral stage (ordinal variable, Figure 12 ...
survival gui cancer kaplan-meier written 2.7 years ago by kmezhoud0

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