User: theobroma22

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theobroma22540
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Posts by theobroma22

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Comment: C: Does BioMart based go-terms contain any insignificant go-terms ?
... "Please be mindful of language barriers of the OPs." I know biomart very well. This is why my answer is about gene enrichment specifically and NOT about BiomaRt. But, yes I see your point. ...
written 1 day ago by theobroma22540
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Answer: A: Remove outlier from ExpressionFeatureSet - Outliers
... If you download CEL files to your directory you can load whichever you want in R using the oligo package. ...
written 1 day ago by theobroma22540
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Answer: A: Does BioMart based go-terms contain any insignificant go-terms ?
... There is a P-value associated with the gene enrichment of each determined GO term. So, there is an expected number of genes for each GO term, and the enrichment can be more or less than what's expected. As for any other analysis, go ahead and choose a P-value cut-off like 0.05 to demonstrate signifi ...
written 1 day ago by theobroma22540
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Answer: A: photosynthesis genes of the plant 'arabidopsis'
... > can I use the photosynthesis pathways (map00195 and map00710) from kegg database to know all the related genes? Yes, you can. You can also use GO terms like photosynthesis. > how I do that with R? There are many R packages like BiomaRt and KEGGREST that are useful for what you want to d ...
written 2 days ago by theobroma22540
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Answer: A: DE analysis using single cell RNA-seq data
... http://www.rna-seqblog.com/cellview-interactive-exploration-of-high-dimensional-single-cell-rna-seq-data/ ...
written 14 days ago by theobroma22540
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Comment: C: How to find which residues in a protein which are targetable by CRISPR
... So, shouldnt you use a genome browser to help answer your question? ...
written 14 days ago by theobroma22540
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Comment: C: CNV detection for plant genome
... There a few CNV-related R packages available on the Bioconductor website. After reading the vignettes for the CNV and CNVtools packages it seems these can handle any genome, or for which an SNP array was used. ...
written 15 days ago by theobroma22540
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Comment: C: How to find which residues in a protein which are targetable by CRISPR
... > The problem is I dont have any idea how to determine which residues whose codons are too far away (greater than 21 or 11 nt) from the PAM motif! You don't mention the organism, so my question is 'is the genome sequence not available for your organism?' ...
written 15 days ago by theobroma22540
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Comment: C: Extracting two matched columns from a file
... What if you just write, mg, in the command line? And since this is a vector it should be length(mg), not dim(mg)! ...
written 20 days ago by theobroma22540
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Answer: A: Extracting two matched columns from a file
... Try mg= intersect(data1$Gene , data2$Gene ) UPDATE: Look at it like this. Here are two dataframes of the same size: data1 = data.frame(ID = LETTERS[1:10], Gene = LETTERS[10:1]) data2 = data.frame(ID = LETTERS[8:18], Gene = LETTERS[18:8]) mg1 = intersect( data1$Gene, data2$G ...
written 20 days ago by theobroma22540 • updated 20 days ago by Ram11k

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Scholar 15 days ago, created an answer that has been accepted. For A: Creating a targets matrix
Scholar 20 days ago, created an answer that has been accepted. For A: Creating a targets matrix
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Creating a targets matrix
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Scholar 6 weeks ago, created an answer that has been accepted. For A: Creating a targets matrix
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Scholar 8 weeks ago, created an answer that has been accepted. For A: Creating a targets matrix
Scholar 9 weeks ago, created an answer that has been accepted. For A: Creating a targets matrix
Scholar 3 months ago, created an answer that has been accepted. For A: Creating a targets matrix
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Creating a targets matrix

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