User: Smandape

gravatar for Smandape
Smandape60
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60
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United States
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4 days, 19 hours ago
Joined:
7 years, 5 months ago
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Posts by Smandape

<prev • 18 results • page 1 of 2 • next >
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Answer: A: How to integrate GSEA (genes) and MSEA (metabolites) analysis ?
... One way I am doing it is by using pathways those represent metabolites and genes in them. This way I am using the same pathways as background for running enrichment analysis. Although, for doing this I had to write my own enrichment analysis script. I didn't find any tool that will do what I want. ...
written 10 weeks ago by Smandape60
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BLAST RNASeq assembled fastq file to a gene sequence
... Hello Experts, I have de novo assembled RNASeq data. I want to see if my gene of interest shows up in this assembled data. The assembled RNASeq data is about 50GB. Would BLAST2BLAST / CLC genomics be a good option to find matching sequence in RNASeq data? What would be a good way to find my ge ...
gene rna-seq blast written 9 months ago by Smandape60
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Answer: A: How to link TCGA/GDC HTSeq or FPKM data with clinical data?
... There is a similar thread, [here][1], that mentions how to map UUIDs to TCGA barcode might answer your question. [1]: https://www.biostars.org/p/215175/ ...
written 2.0 years ago by Smandape60
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Answer: A: How to download Protein Expression data through manifest file from TCGA ?
... Maybe this is too late to reply but might help someone else as well. All the TCGA's data is available via Genomic Data Commons (GDC) portal. For downloading files using a manifest file you can use their Data Transfer Tool ([here][1]). It is easy to use and their documentation mentions in detail how ...
written 2.0 years ago by Smandape60
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Comment: C: Clutering Using Mcl Algorithm
... Can you open this file in notepad++? ...
written 5.4 years ago by Smandape60
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What Next After Contigs?
... I have contigs from a bacterial genome sequence. I am trying to find what would be the reference for this strain or where does it belong to in the phylogenetic tree. Also, what would be a good way to stitch them together? I did BLAST with individual contigs and also with all contigs together but I a ...
phylogeny assembly phylogenetics contigs written 5.4 years ago by Smandape60 • updated 5.4 years ago by sentausa630
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Comment: C: Convert Pmids To Nihmsid And Pmcid Using Eutils
... @Neilfws: Thank you so much for this direction. I didn't know how to move forward with my question. I also tried to put this question in Stackoverflow with possibility of webscraping but, no one replied and I was clueless how to do it with scrappy and other libraries in python. I was trying to get t ...
written 5.4 years ago by Smandape60
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Convert Pmids To Nihmsid And Pmcid Using Eutils
... I would like to know if I can convert PMID to NIHMSID, if there is no PMCID associated with that PMID and retrieve both of them if PMCID exists. I want to do this programmatically may be using eutils if possible. I know about this link http://www.ncbi.nlm.nih.gov/pmc/pmctopmid/ that will do the work ...
webservice eutils written 5.4 years ago by Smandape60 • updated 5.4 years ago by Neilfws48k
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Comment: C: Finding Genome Coverage Using Random Reads
... Thank you. Well, I got the same answer but I was not sure if its correct. ...
written 7.2 years ago by Smandape60
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Comment: C: Finding Genome Coverage Using Random Reads
... lol..I also posted it at http://www.daniweb.com/software-development/computer-science/threads/399022/1710513#post1710513 ...
written 7.2 years ago by Smandape60

Latest awards to Smandape

Supporter 21 months ago, voted at least 25 times.
Popular Question 3.7 years ago, created a question with more than 1,000 views. For What Next After Contigs?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For How To Randomly Select 2 Sequences From Fasta Format In Perl?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Local Copy Of Pubmed
Popular Question 5.4 years ago, created a question with more than 1,000 views. For How To Randomly Select 2 Sequences From Fasta Format In Perl?
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Convert Pmids To Nihmsid And Pmcid Using Eutils
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Local Copy Of Pubmed
Student 5.4 years ago, asked a question with at least 3 up-votes. For Local Copy Of Pubmed

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