User: hodayabeer

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hodayabeer0
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Posts by hodayabeer

<prev • 9 results • page 1 of 1 • next >
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Error in BioMartVersion
... Hi, I am trying to convert between EntrezID to gene symbol using 'bioMart' package and the following function: source("https://bioconductor.org/biocLite.R") library('EnrichmentBrowser') library('biomaRt') convert_to_genes_symbol<-function(ptwy_genes){ library('Enrichm ...
gene R biomart gene symbol entrezid written 25 days ago by hodayabeer0 • updated 24 days ago by James Ashmore2.3k
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Comment: C: hierarchial clustering of genes- identify number of clusters
... Thank you for your answer. What I am trying to do is to write a code that will identify number of clusters in a lot of datasets, simultaniously. Therefore, I am trying to find a systematic way to do that, without the involvment of human. So how can I apply your suggestion in a R code, and let the a ...
written 6 weeks ago by hodayabeer0
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hierarchial clustering of genes- identify number of clusters
... Hi all, I have a data set where the rows are genes and columns are phylogenetic profiling scores. I clustered this dataset of genes in Hierarchial Clustering in R, and got a dendogram of the hclust() output. I need to identify the number of clusters, so that genes in the same cluster will be very ...
gene hierarchial clustering cluster R written 6 weeks ago by hodayabeer0 • updated 6 weeks ago by Kevin Blighe13k
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Comment: C: How to prevent blastp from aligning small parts of query sequence and scoring th
... how can I extract only the results where the alignment lengths is equal or close to the query / subject length? ...
written 4 months ago by hodayabeer0
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Comment: C: How to prevent blastp from aligning small parts of query sequence and scoring th
... how can I extract only the results where the alignment lengths is equal or close to the query / subject length? ...
written 4 months ago by hodayabeer0
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Comment: C: How to prevent blastp from aligning small parts of query sequence and scoring th
... but I want to get only full alignments of the query sequence ...
written 4 months ago by hodayabeer0
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How to prevent blastp from aligning small parts of query sequence and scoring that high?
... Hi, I was blasting proteome of yeast against a large database of Archaea. Something is wrong with the results because I got too large P Identity for too much proteins. I assume that the problem is that blast scores small parts of the query sequence once it found an alignment to that, and therefore ...
alignment sequence blast written 4 months ago by hodayabeer0
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Comment: C: Scientific Names In Blast Output And Databases
... Hi, I was facing the same problem and then I realized that the blast command must be in the same directory as the nr database and the 2 taxdb files (.bti , .btd). It solved the problem. Good luck! ...
written 5 months ago by hodayabeer0
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Comment: C: Species identification via gilist
... Hi Yi-Ting, can I ask how did you get this bacteria gi list from? I am trying to download it directly from the NCBI (by 'save to file' -> GI List etc...) but it failes due to timeout error.. Do you have an easy way to do that? tnx in advance ...
written 5 months ago by hodayabeer0

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