User: hkarakurt

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hkarakurt10
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Posts by hkarakurt

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... I just checked and MS_getPathIds command is not working. It is in reference manual but R cannot find the function. ...
written 3 days ago by hkarakurt10
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Comment: C: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... I will check the package. Thank you so much. ...
written 3 days ago by hkarakurt10
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Comment: C: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... Yes these are the data frames I want. Actually format is not really important but mostly it should be a table which includes a column for gene and a column with associated compound.   Thank you for your answer. ...
written 3 days ago by hkarakurt10
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Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... Hello, I need to build a Gene-Metabolite (Compund) and Metabolite - Pathway network for Streptomyces coelicolor from KEGG. I tried KEGGREST package for R but I only can download Gene - Pathway network. Anyone knows how can I download this network with KEGGREST or any other packages?   Thank you, ...
keggrest kegg written 4 days ago by hkarakurt10 • updated 3 days ago by 7kemZmani10
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How to download All Protein Protein Interactions of an organism with Bioconductor
... Hello everyone, I need to download whole protein-protein interaction network of Mus musculus. I downloaded from STRING but the file is too big to manipulate (about 12 million lines). I need to delete some interactions with low confidence score but I cannot open this file with Matlab, R, Python or E ...
mus musculus stringdb ppi written 16 days ago by hkarakurt10 • updated 16 days ago by damian.szk0
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Differential Coexpression Analysis
... Hello everyone, I want to do a differential coexpression analysis to a microarray data. My data have rows for genes and columns for conditions. 30 control and 28 disease columns.  I checked some packages such as WGCNA but I think they don't take expression data as input. Anyone has any advice, tu ...
differential gene expression correlation coexpression differential analysis written 6 weeks ago by hkarakurt10 • updated 6 weeks ago by Peter Langfelder1.4k
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Comment: C: Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
... Yes there is only one supplement file and it is the Counts file. Mostly there are RAW_data files in supplemental files but this data is different. Probably I will use counts data for analyses. Thank you for answer. ...
written 8 months ago by hkarakurt10
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Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
... Hello, I am new at RNA-Seq data analysis and I want to analyze the data and do some analyses such as finding differentially expressed genes. My data set is from NCBI GEO and coded as GSE80336. Link is here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80336 I see data is not normalized. I ...
rnaseq limma geoquery edger rna-seq written 8 months ago by hkarakurt10 • updated 8 months ago by Sean Davis21k
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Bioconductor for predicting transcription factors from a gene list?
... Hello, I have about 150 human genes. I want to build a transcription factor-gene network so I need to find which TF binds to which gene? Is there any bioconductor package for finding possible transcription factors for gene list? Thank you. ...
transcription transcriptdb written 11 months ago by hkarakurt10
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lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
... Hello, I am new at Biocondurctor and trying to read, normalize and analyze a expression data from Illumina platform. I have raw data (non-normalized) as text format and I want to read it with lumiR() command but when I try, I have this error: Error in gregexpr("\t", dataLine1)[[1]] : subscript ou ...
normalization beadarray lumi illumina written 11 months ago by hkarakurt10

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