User: hkarakurt
hkarakurt • 10
- Reputation:
- 10
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- New User
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- Last seen:
- 2 days, 11 hours ago
- Joined:
- 11 months, 2 weeks ago
- Email:
- h********@gtu.edu.tr
Posts by hkarakurt
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... I just checked and MS_getPathIds command is not working. It is in reference manual but R cannot find the function.
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written 3 days ago by
hkarakurt • 10
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... I will check the package.
Thank you so much.
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written 3 days ago by
hkarakurt • 10
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... 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.
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written 3 days ago by
hkarakurt • 10
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... 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,
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... 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 ...
written 16 days ago by
hkarakurt • 10
• updated 16 days ago by
damian.szk • 0
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... 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 ...
written 6 weeks ago by
hkarakurt • 10
• updated 6 weeks ago by
Peter Langfelder • 1.4k
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... 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.
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written 8 months ago by
hkarakurt • 10
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... 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 ...
written 8 months ago by
hkarakurt • 10
• updated 8 months ago by
Sean Davis ♦ 21k
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... 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.
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written 11 months ago by
hkarakurt • 10
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... 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 ...
written 11 months ago by
hkarakurt • 10
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