User: saber mohammadi

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Posts by saber mohammadi

<prev • 13 results • page 1 of 2 • next >
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iFeature does not work
... Hello everybody. I'm trying to extract some features from my protein sequence dataset. I'm using iFeature toolkit. When I run iFeature on my system, it gives me a non-sense output. It provides an output file with a lot of zeros. It seems like it doesn't calculate anything. By the way, I'm working o ...
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Comment: C: how to increase cd-hit capacity
... I'm trying to make a dataset of mesophile proteins. I'm going to use cd-hit representative sequences as a dataset in machine learning methods. So they shouldn't be similar to avoid redundant information during the learning step. I set word-size=2 because I read that on cd-hit user's guide: [cd-hit ...
written 20 days ago by saber mohammadi0
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Comment: C: how to increase cd-hit capacity
... Thanks for responding. cd-hit -i ../TP_MP_Project/Mesophiles_final.fasta -o ../TP_MP_Project/cdhit_output -c 0.4 -n 2 -M 16000 -T 8 >& log & This is the command I run. I got no output. Actually I run it on a Linux server, after a while I realize that cdhit is not running and also th ...
written 20 days ago by saber mohammadi0
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how to increase cd-hit capacity
... Hello, everybody I have a fasta file which includes 441648 sequences. I'm running cdhit on this amount of sequences. But I get no output. I think it's because my fasta file is too big and cdhit can't handle this amount of data. Am I right? If I am so is there any way that I could increase cdhit capa ...
seqeunce identity cdhit written 20 days ago by saber mohammadi0
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Comment: C: cd-hit log file
... Would you please help me with GNU screen? I have no idea how to use it. I use `cd-hit -i ../TP_MP_Project/Mesophiles_final.fasta -o ../TP_MP_Project/Output -c 0.4 -n 2 -M 16000 -T 8` command to start my job ...
written 27 days ago by saber mohammadi0
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cd-hit log file
... Hey everybody. I'm trying to cluster set of sequences by cd-hit. I'm using cd-hit on linux by the way. I'm wondering how can I know the progress of my job while I've sent my job to background. Is there any log file?? Can anyone help me with that?? Thanks. ...
sequence similarity cdhit written 27 days ago by saber mohammadi0 • updated 27 days ago by Mensur Dlakic1.3k
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Text mining software
... Hey, everybody. I'm looking for some text mining software which has GUI(Graphical User Interface). Actually, I want a software, not a tool or package in R or Python. Is there anyone to help me on this? ...
text-mining written 2.6 years ago by saber mohammadi0 • updated 2.6 years ago by Michael Dondrup46k
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Comment: C: retrieving pubmed abstracts
... Yes. There is should be a way. isn't there? ...
written 2.6 years ago by saber mohammadi0
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Comment: C: retrieving pubmed abstracts
... Yes, I can provide the PMID to RISmed package and download the respective abstract. But I want to retrieve all the PubMed's abstracts, not a particular one. And I also want to retrieve all these data by R because I should write a program for my text mining project and the first step is to retrieving ...
written 2.6 years ago by saber mohammadi0
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retrieving pubmed abstracts
... hey, everybody. I have a text mining project and I have to write a program in R. I'm using the RISmed package to retrieve the articles abstract. I've got a problem here. I want to to use RISmed package or any other package in R in order to download all the PubMed's abstracts, not a particular abstr ...
R written 2.6 years ago by saber mohammadi0 • updated 2.6 years ago by Pierre Lindenbaum123k

Latest awards to saber mohammadi

Popular Question 17 months ago, created a question with more than 1,000 views. For what dose taxonomic distribution mean?
Popular Question 17 months ago, created a question with more than 1,000 views. For retrieving pubmed abstracts
Popular Question 19 months ago, created a question with more than 1,000 views. For retrieving data from Pubmed by RISmed package in R

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