User: Alejandro Jimenez Sanchez

Reputation:
80
Status:
Trusted
Location:
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
Website:
http://miller-lab.org/
Last seen:
3 hours ago
Joined:
1 year, 9 months ago
Email:
a***********************@cruk.cam.ac.uk

I am a graduate student interested in cancer research both from the dry and wet lab. Currently, I am working on a cancer immunoediting model.

Posts by Alejandro Jimenez Sanchez

<prev • 23 results • page 1 of 3 • next >
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Answer: A: Install ABSOLUTE Error
... I've found the solution. I downloaded again the tar.gz file and installed the package from source by doing: R CMD INSTALL ABSOLUTE_1.0.6.tar.gz In the directory where the tar.gz file was located. Then, doing: library(ABSOLUTE) Works. I'll leave this here in case someone needs it in th ...
written 19 days ago by Alejandro Jimenez Sanchez80
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Install ABSOLUTE Error
... Hello, A while ago I ran [ABSOLUTE][1] and I have the script I used. I want to run it again but when I do: library(ABSOLUTE) I get: Error in library(ABSOLUTE) : there is no package called ‘ABSOLUTE’ If I do: install.packages("ABSOLUTE", lib="/Library/Frameworks/R.framework/Versio ...
absolute R package written 19 days ago by Alejandro Jimenez Sanchez80
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6 follow
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Data repository for Whole Exome Sequencing
... Hi, I was wondering if there is any data repository like [GEO][1] for Whole Exome Sequencing data. Thanks for your help. Alejandro UPDATE If anyone has the same question, it was quite easy to upload the bam files to the [SRA database][2]. Thanks for the suggestions! [1]: https://www.ncbi.nl ...
geo database wes written 3 months ago by Alejandro Jimenez Sanchez80
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Answer: A: Where Can I Download All Exons Of The Human Genome In Fasta Format (One Big File
... If anyone is looking for the same but for GRCh37 [here][1] is the link. [1]: http://grch37.ensembl.org/biomart/martview/35a76216fa3fb9762f17c7c2cf5aecbf ...
written 7 months ago by Alejandro Jimenez Sanchez80
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Answer: A: Hypergeometric Test On Gene Set
... I think method 1 is the correct one, because. Method 1 gives the same result as this site: https://www.geneprof.org/GeneProf/tools/hypergeometric.jsp Method 2 gives a different result. ...
written 11 months ago by Alejandro Jimenez Sanchez80
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Is it possible to include all possible gene transcripts affected by a mutations using vcf2maf?
... To convert VCFs to MAFs I use the very well documented tool [vcf2maf][1]. In the introduction it says: > To convert a VCF into a MAF, each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect. This selection of a single effect per variant, is often s ...
vcf2maf written 11 months ago by Alejandro Jimenez Sanchez80
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Comment: C: How to run multiple jobs with GNU parallel with multiple arguments?
... The --verbose output is: ./script.sh argA argB1 argC ./file.txt ./script.sh argA argB2 argC ./file.txt I don't understand why it works only for the first one, while when it comes the second line ./script.sh gives the error `predict_binding.py: error: incorrect number of arguments` I am us ...
written 12 months ago by Alejandro Jimenez Sanchez80
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Comment: C: How to run multiple jobs with GNU parallel with multiple arguments?
... If I do: parallel --verbose ./script.sh ::: argA ::: `cat vals.txt` ::: argC ::: ./file.txt It works only for one job and the other I get the error: `.script.sh: error: incorrect number of arguments` And if I use the same vals.txt file and do: cat vals.txt | parallel --verbose ./script.s ...
written 12 months ago by Alejandro Jimenez Sanchez80
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Comment: C: How to run multiple jobs with GNU parallel with multiple arguments?
... Thanks for your reply. I've just tried it and it didn't work. :( I created file2.txt with the following in it: argB1 argB2 As I understand your suggestion, I did: parallel --verbose ./script.sh ::: argA ::: file2.txt ::: argC ::: file1.txt The command was passed as: ./script.sh ...
written 12 months ago by Alejandro Jimenez Sanchez80
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How to run multiple jobs with GNU parallel with multiple arguments?
... Hi I have a burning question, I want to run a script named "predict_binding.py". Its syntax is: ./predict_binding.py [argA] [argB] [argC] ./file.txt file.txt has a column of strings with the same length: string_1 string_2 string_3 ... string_n predict_binding.py works ...
gnu parallel written 12 months ago by Alejandro Jimenez Sanchez80 • updated 12 months ago by malteherold20

Latest awards to Alejandro Jimenez Sanchez

Scholar 19 days ago, created an answer that has been accepted. For A: Install ABSOLUTE Error
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to run multiple jobs with GNU parallel with multiple arguments?
Popular Question 7 months ago, created a question with more than 1,000 views. For ABSOLUTE to estimate tumour purity from WES data
Student 11 months ago, asked a question with at least 3 up-votes. For Protein database for TCGA MAF files
Supporter 12 months ago, voted at least 25 times.
Autobiographer 21 months ago, has more than 80 characters in the information field of the user's profile.

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