User: amy.bashir

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amy.bashir50
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Posts by amy.bashir

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Tools for investigating the correlation of differential gene expression & histon
... I think BETA (http://cistrome.org/BETA/) is well suited for this task. ...
written 10 days ago by amy.bashir50
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Answer: A: WGCNA analysis for normalised data expression data sets
... Trait data is biological features associated with each animal that the sample is derived from. For example, if you are studying the gene co-expression networks underlying a cardiovascular disease, trait data would be the things like weight, blood pressure and blood cholesterol level of each patient/ ...
written 11 days ago by amy.bashir50
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Comment: C: Breakdancer : Can't locate Statistics/Descriptive.pm in @INC while trying to run
... I will just say up front that I am really new to all this too... Do you have root access on the system you are using, i.e. can you use sudo? Maybe it would be easier to follow the instructions [here][1] to set up a new place where you can use CPANminus to install modules. [1]: https://stack ...
written 13 days ago by amy.bashir50
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Answer: A: Breakdancer : Can't locate Statistics/Descriptive.pm in @INC while trying to run
... I remember having a similar problem, it was because I had two versions of Perl installed so the paths got all messed up. Is the Statistics/Descriptive module in one of the paths listed in @INC: /usr/local/lib64/perl5 OR /usr/local/share/perl5 OR /usr/lib64/perl5/vendor_perl OR /usr/share/perl5/ve ...
written 13 days ago by amy.bashir50
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hello, As you recommended, I tried this command to prepare the goa_uniprot_all database: nohup ./prepare_database -db=GO_all -org=goa_uniprot_all & I also tried to use "update" mode along with a gene list, but in both cases, I see that the database files get stuck in the state as shown i ...
written 25 days ago by amy.bashir50
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Comment: C: Are TPM values generated by different programs comparable?
... Oh, that's a great idea. Thank you very much! ...
written 25 days ago by amy.bashir50
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Are TPM values generated by different programs comparable?
... Hello! I am currently analyzing a set of RNA-seq data. I first used StringTie to calculate the TPM values of reads that are mapped to the genome (a non-model organism). Then, for the ~5% of reads that were not mapped to the genome, I used Trinity to *de novo* assemble the reads and then used Kallis ...
stringtie tpm kallisto written 25 days ago by amy.bashir50 • updated 25 days ago by h.mon8.7k
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Great, thank you very much, I am trying that now! ...
written 27 days ago by amy.bashir50
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hello! I started the prepare_database job for goa_uniprot_all about 9 hours ago when I saw your answer. This is the command I used: nohup ./prepare_database -db=GO_BP -org=goa_uniprot_all The database seems to have been downloaded without problem, but it's been stuck without any change after ...
written 28 days ago by amy.bashir50
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Thank you very much for your quick reply! I will try that! ...
written 28 days ago by amy.bashir50

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Scholar 11 days ago, created an answer that has been accepted. For A: WGCNA analysis for normalised data expression data sets

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