User: bioinformatics

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Posts by bioinformatics

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Best way to link drugs to diseases prefferably using R
... ​Hello ! Does anyone know good ways to calculate diseases for each drug in a list ? ​Preferably in R in a way we can select on different characteristics. ​We know about DrugVsDisease, but is there something similar or better ? ​ ​Best Regards, ​ ...
drug written 4 days ago by bioinformatics10
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rpubchem is not working , or is it ?
... Hello Word, I would like to use rpubchem to search for information about drug candidates, however i seem to encounter a problem when i use an example provided by a function. I have problems with all the functions I want to use, they give similar errors as the following : > aids <- find.ass ...
rpubchem written 15 days ago by bioinformatics10
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Comment: C: Search for Drugs related to results of differential expression analysis using RN
... Dear Efstathios, I would like to thank you for your previous reply, the website ( tool ) you mentioned seems to be working very well. There is also documentation available on how to use API's and drug candidates can also be searched using API. This really did help a lot !   ...
written 20 days ago by bioinformatics10
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Comment: C: Search for Drugs related to results of differential expression analysis using RN
... Dear Efstathios, Thank you for your quick and helpful reply. We will have a look at the L1000CDS2, which seems to be a very interesting and easy way to get to a solution for our described problem. The question we provided was specifically in regards to bioconductor packages, as when used we want ...
written 20 days ago by bioinformatics10
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Search for Drugs related to results of differential expression analysis using RNA-seq
... Hello World, We have a list of differentially expressed genes from a RNA-seq experiment, including the fold changes p-values etc. Our goal is to link these genes to drugs that have influences on these genes. This could lead to potential drugs that can help to induce or delay a diseased phenotype(m ...
rnaseq gcmap drugvsdisease gcmapweb written 20 days ago by bioinformatics10 • updated 19 days ago by saezrodriguez0
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Find drugs influencing specific genes
... Hello, We have performed transcriptome analysis , which resulted in a collection interesting genes. The ultimate goal would be to find drugs that have the ability to influence these genes of interest. After research we came up with the following website ( tool ) : https://portals.broadinstitute. ...
drug development written 11 weeks ago by bioinformatics10
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Drug datasets for RNA-seq
... ​Hello everyone ! We have done an rna-seq experiment and found some differentially expressed(de) genes. We want to test some drugs in our lab to find interesting ones for further analysis. Because there are so many drugs it would be cool to compare the differentially expressed genes we found to alr ...
data rna-seq written 4 months ago by bioinformatics10 • updated 4 months ago by Gordon Smyth30k
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Answer: A: EdgeR multiple factor design question
... Dear Aaron, Thank you for your quick and straight to the point answer. There are some parts where I still have some doubt. For example you propose : con <- makeContrasts(treatedY - treatedN, levels=design) And put this into the contrast of glmLRT. Does this mean that the steps : dge <- ...
written 5 months ago by bioinformatics10
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EdgeR multiple factor design question
... I have rna-seq data with three facors : treated , time, temperature I want to get differential expressed genes for the treatment, but the design should also account for the temperature and time.   I have created the following setup:    d <- DGEList(counts = countTable)  #~ #normalization mu ...
edger design matrix written 5 months ago by bioinformatics10
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EdgeR two condition problem
... Hello !    I have used DESeq and EdgeR to get differentially expressed genes.    For DESeq it is possible to put a design with more conditions.  This is important because the data i used has    for example treated and untreated columns. But also differences in  cells types. And also the way ...
edger written 5 months ago by bioinformatics10 • updated 5 months ago by Aaron Lun14k

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