User: 5utr

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5utr350
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350
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Trusted
Location:
Canada
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1 week, 3 days ago
Joined:
5 years, 11 months ago
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Posts by 5utr

<prev • 38 results • page 1 of 4 • next >
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Answer: A: R partial string matching with constraints
... Probably there is a more concise way but this works: queries=c('GTASQ','QSD','DRARTK','GTASQW') subject=c('ASQSDRA') lapply(queries,function(X) #peptides have to fall completely into sequence grepl(X,subject) | # or start with the sequence end any(unlist(lapply( ...
written 5 weeks ago by 5utr350
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R partial string matching with constraints
... I would like to find matches between two list of AA strings so that 1 of these 3 rules is matched : 1) query string has to be a substring of subject string 2) query string has to end with the same pattern the subject string starts (any number of characters) 3) query string has to start with the s ...
pattern matching R grep written 5 weeks ago by 5utr350
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Comment: C: DEseq on mixed cohort with and without replicates
... Thank you I forgot to mention collapseReplicates but from my understanding it is meant to merge "multiple sequencing runs of the same library" and what I have are different preps from the same tumor biopsy. Would it still apply? ...
written 9 weeks ago by 5utr350
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DEseq on mixed cohort with and without replicates
... I have a cohort were multiple tumors, 5 from subtype A and 5 from subtype B, were sequenced. I want to run a DE analysis of subtype A vs subtype B. The non trivial part is that some tumor were sequenced in replicates while others as single samples. What is the best way to merge replicate samples bef ...
deseq rna-seq written 9 weeks ago by 5utr350
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Answer: A: How to identify transcription factors (TFs) from expression data comparison?
... Are these human cell lines? If you are interested in identifying TFs that might regulate a differentially expressed gene you can calculate the correlation between the expression profile of your gene and a list of TFs. Considering that the expression profile only includes 10 samples you probably woul ...
written 4.5 years ago by 5utr350
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Answer: A: GEO - Cannot find processed gene expression data ?
... You can find the gene RPKM values for the different samples in `GSE56227_RAW.tar` in the download section. Sometimes the processed gene expression is in the Series Matrix File but usually for array data. ...
written 4.5 years ago by 5utr350 • updated 5 months ago by RamRS27k
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Comment: C: How to perform correlation between unmatched miRNA and mRNA data?
... First you need to exclude the samples that are not in both datasets and then you can calculate the correlation on the overlapping subset. Since you are using R you can merge the two matrix and then calculate Spearman correlation between all miRNAs and mRNA ...
written 4.5 years ago by 5utr350 • updated 5 months ago by RamRS27k
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Comment: C: How to perform correlation between unmatched miRNA and mRNA data?
... I think you should explain what you mean with 'unmatched', you can only calculate correlation on matching samples. ...
written 4.5 years ago by 5utr350
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Answer: A: Probing specific protein amino acid position changes in R
... There are indeed many different function that you can use to manipulate strings, this is an example using Biostrings: #load package library(Biostrings) #reference sequence standardseq<- AAString("MARKSLEMSIR") #query sequences seq1 <- AAString("MARKSLEMSER") seq2 & ...
written 4.5 years ago by 5utr350 • updated 5 months ago by RamRS27k
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Answer: A: How to get coordinates from UCSC Genome Browser
... When you enter the gene name genome browser offers you with a list of genes and transcripts that match your query, each one has the coordinates for the assembly that you selected. Alternatively you can go to Table browser and download a flat table that you can customize: https://genome.ucsc.edu/cgi ...
written 4.5 years ago by 5utr350 • updated 5 months ago by RamRS27k

Latest awards to 5utr

Scholar 5 weeks ago, created an answer that has been accepted. For A: Creating subgraph using igraph
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Scholar 4.5 years ago, created an answer that has been accepted. For A: Creating subgraph using igraph
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Creating subgraph using igraph
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