User: hodayabeer

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hodayabeer10
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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 15 months ago by hodayabeer10 • updated 15 months ago by James Ashmore2.6k
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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 16 months ago by hodayabeer10
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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 16 months ago by hodayabeer10 • updated 16 months ago by Kevin Blighe42k
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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 19 months ago by hodayabeer10
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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 19 months ago by hodayabeer10
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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 19 months ago by hodayabeer10
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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 19 months ago by hodayabeer10
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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 20 months ago by hodayabeer10
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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 20 months ago by hodayabeer10

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