User: maureen.pittman

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Posts by maureen.pittman

<prev • 5 results • page 1 of 1 • next >
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Retired Ensembl genes - should I identify their successors?
... Hello, I am running WGCNA analysis on public RNA-seq expression data. Some of the gene IDs are in Entrez, others in Ensembl. I want them all in Entrez. I tried using both NCBI and BioMart to convert the Ensembl IDs, but it seems that any way you cut it, around 3000 out of 20,000 genes don't have ma ...
wgcna ensembl id id conversion entrez id written 2.7 years ago by maureen.pittman0
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Can I use a matrix of Pearson Correlation Coefficients as input into WGCNA?
... Hello, I am using public expression data to create weighted co-expression networks in WGCNA. One source I was hoping to use ([COXPRESdb][1]) has aggregated expression data in the form of Pearson correlation coefficients calculated for all pairwise comparisons of gene-expression values. Would this m ...
pearson correlation wgcna coxpresdb pcc written 2.9 years ago by maureen.pittman0 • updated 2.3 years ago by Lluís R.810
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Is there a way to access sample phenotype information in SRAdb?
... Hello all, I am currently trying to find the most efficient way to obtain RNA-seq data for input into a co-expression network. This means I'll be downloading multiple runs from ~50 experiments (~700 runs in all). So far it has seemed like SRAdb is the best way to do this, by bulk-selecting and down ...
metadata sradb phenotype written 2.9 years ago by maureen.pittman0
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Using bioconductor GEOmetadb to find RNA-seq datasets
... Hello,   I'm trying to collect RNA-seq datasets for co-expression network analysis. I've been using both SRAdb and GEOmetadb to search and have experienced limited success with both, for different reasons.   Using SRAdb, I was able to isolate all RNA-seq experiments (from a column describing "li ...
geometadb geo bioconductor sradb rna-seq written 3.0 years ago by maureen.pittman0
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How to create a table from a list while preserving attributes
... Hello all, I am trying to use R to create a table that links all KEGG orthology IDs to all related Entrez genes. In theory this can be done using the KEGGREST package from bioconductor.  I have a list of all the KEGG orthology IDs, which I want to convert to Entrez IDs using the function keggConv. ...
R keggrest creating dataframes from lists written 3.3 years ago by maureen.pittman0

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Popular Question 2.7 years ago, created a question with more than 1,000 views. For Can I use a matrix of Pearson Correlation Coefficients as input into WGCNA?

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