User: brett.vanderwerff

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Posts by brett.vanderwerff

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Comment: C: Bioinformatics Workstation Suggestions
... We use a workstation with 6 cores (12 threads) and 64GB RAM for our human RNA-seq samples. It has been great for us (most intense thing we use is STAR). I can't speak for scRNA-seq. ...
written 5 weeks ago by brett.vanderwerff130
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Comment: C: how to download pubmed article abstracts for multiple terms using programming?
... You could have a look at pubtator and some of the tools that are growing around it. Pubtator is a database of all the pubmed abstracts and is actually annotated for some terms. I know its not full papers but might be worth a look. ...
written 9 weeks ago by brett.vanderwerff130
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Comment: C: Extract and ADD text information
... If you know some basic programming you can use python to read a file in and append every new line to a list. you can then save only the elements that you want and using string slicing to further carve what you what out of each element. Python is really REALLY good with text stuff and this project w ...
written 9 weeks ago by brett.vanderwerff130
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Can two Kaplan-Meier survival curves cross and still have proportional hazards?
... The way I understand cox regression is that it works on the assumption that the hazard curves for groups are proportional and as such do not cross on a plot. So I have this experiment that is looking at the effect of low or high expression levels of gene 1 and gene 2 on survival of cancer patients ...
cox survival regression written 9 weeks ago by brett.vanderwerff130
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Answer: A: How to select only protein coding mRNAs from a really long list of ENSG IDS
... this is what I ended up with if anyone is curious: library(biomaRt) ensembl = useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") example_ids = c("ENSG00000172927", "ENSG00000224713", "ENSG00000135269", "ENSG00000272555", "ENSG00000013588") res <- getB ...
written 9 weeks ago by brett.vanderwerff130
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How to select only protein coding mRNAs from a really long list of ENSG IDS
... I have an R dataframe with a column of ENSG IDs. I believe it contains non-protein coding IDs that I do not want I only want to keep the rows that correspond to protein coding mRNAs I am looking for a source of ENSG IDs (list or similar) that only contains IDs corresponding to protein coding mRN ...
ensg ensembl rna ids written 9 weeks ago by brett.vanderwerff130
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How to know if high expression of a gene is really a good independent marker for poor prognosis in cancer?
... This is kind of a general question that I have been curious about for a while. Please consider my example: I have a gene that seems like it should be associated with pro-cancer effects based on the literature. I go ahead and mine rna-seq samples from cancer patients and code them as "high expresse ...
tcga cox survival rna-seq regression written 10 weeks ago by brett.vanderwerff130 • updated 10 weeks ago by omg what am I doing60
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Comment: A: Python code for extracting values from an Excel database?
... Look at pandas which is very good at working with excel sheets as a starting point: https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_excel.html EDIT: Sorry I meant this to be a reply I don't know how to delete as answer :/ ...
written 10 weeks ago by brett.vanderwerff130
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Comment: C: Survival analysis with gene expression
... Kevin, I actually do have a quick question related to this now that I think about it (if you have time). I see you have your expression factor with three levels: survplotdata$CXCL12 <- factor(survplotdata$CXCL12, levels = c('Mid', 'Low', 'High')) In theory this was supposed to produc ...
written 10 weeks ago by brett.vanderwerff130
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Comment: A: Survival analysis with gene expression
... Kevin, Unless there is a problem on my end, I think something may have gotten deprecated here. Running code as is only gives me mid and high curves for both genes. Inspection of > survplotdata <- coxdata[,c('Time.RFS', 'Distant.RFS', > 'X203666_at', 'X205 ...
written 10 weeks ago by brett.vanderwerff130

Latest awards to brett.vanderwerff

Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Bioinformatics Workstation Suggestions
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Hardware requirement for RNA-seq

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