User: aj123
aj123 • 80
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Posts by aj123
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... I was able to resolve this issue by using R Switch and terminal (Mac). Windows appears to have an easier way of doing it. ...
written 8 days ago by
aj123 • 80
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... There seem to be issues with installing GO.db when I try to install the WGCNA package. The error im getting below seems to be very different from other types of error others are getting while doing the same:
> Error: package or namespace load failed for ‘WGCNA’ in loadNamespace(i, c(lib.lo ...
written 8 days ago by
aj123 • 80
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... I have two .csv files. I need to match the 1st rows IDs in one file with the 1st column IDs in another file. im trying this-
If the first file contains a column named "ids" then i do this to extract the sample ids-
first_file_samples <- first_data_frame$ids
And for the second file, if all ...
written 9 days ago by
aj123 • 80
• updated
9 days ago by
bkleiboeker • 10
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Comment:
C: Roast vs GAGE
... modified to make question clearer. ...
written 2.5 years ago by
aj123 • 80
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... I am trying to better understand the fundamental difference between Roast and GAGE -what is the fundamental difference and on what basis do they calculate their P-values? ...
written 2.5 years ago by
aj123 • 80
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... thanks for your response! I will def try exploring these avenues. This is basically case vs control samples (bam files) I have for a human disease. Just doing a DE analyses to see DE genes of interest. Hence was trying to see what other analyses/layers I could add to this. ...
written 2.6 years ago by
aj123 • 80
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Hi,
Im currently doing a simple case vs control analysis on RNA Seq data. I have WGS and SNP data as well. I was wondering what are the different layers and additional analyses I could add on to my work?
thanks! ...
written 2.6 years ago by
aj123 • 80
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... Hi,
Im trying to create a simple RNA Seq pipeline from fastqc to DE in python (or perl). I want to read in a configuration file with paired end data like this:
Sample1 x_1.fastq x_2.fastq
Sample 2 y_1.fastq y_2.fastq
I would want to read it into an array and pull out each filename. P ...
written 4.6 years ago by
aj123 • 80
• updated
4.6 years ago by
Frédéric Bigey • 290
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Comment:
C: Protein interaction network
... ![enter image description here][1]This is for Mouse data. Yes, I am able to load the entire PPI data into Cytoscape. The data is in this form (attached picture). Interactor A and B are the gene names.
[1]: http://s33.postimg.org/peyn8aoen/interaction_sample.jpg ...
written 4.6 years ago by
aj123 • 80
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...
Hello,
I have a list of genes for an organism. I want to pull out the first neighbor i.e the first protein/gene the organism is interacting with from the overall PPI network of the organism. Any suggestions on how I could do this?
...
written 4.6 years ago by
aj123 • 80
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