User: David_emir

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David_emir310
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Posts by David_emir

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Comment: C: Downloding only RNA-Seq Raw counts data from ICGC
... Hope this will help others, code is here. mlr --tsv cut -o -f id4,id1,count2 then reshape -s id1,count2 input.tsv Or datamash --header-in --whitespace crosstab id4,id1 unique count2 < file Thanks for your help ...
written 2 days ago by David_emir310 • updated 2 days ago by ATpoint12k
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Answer: A: Downloding only RNA-Seq Raw counts data from ICGC
... Thanks a lot, Guys, I got a solution for this for cross-tabulation (or pivot table) using GNU Datamash and with Miller, using reshape! Dave ...
written 2 days ago by David_emir310
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Comment: C: Downloding only RNA-Seq Raw counts data from ICGC
... Thanks Vijay, I tried to cut and paste sample_id rows as a column but it gave me a really messed up results. ...
written 3 days ago by David_emir310
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Downloding only RNA-Seq Raw counts data from ICGC
... Hi, I wanted to download RNA-Seq raw counts data from ICGC with samples as columns and gene_symbol as row names. I tried using dplyr but I am not able to get in the proper format. It would be of great help to me if you guys can let me know how to download this. Sincerely, Dave P.S: any package i ...
icgc raw counts written 3 days ago by David_emir310
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Comment: C: Extracting data in a particular Format- only Raw counts in matrix format
... Thanks Devon! I will look into dplyr ...
written 4 days ago by David_emir310
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Extracting data in a particular Format- only Raw counts in matrix format
... I have gene.csv file which is about 1.3 GB in size and has got 300 columns and more than 1 million rows. it looks like following, id1 id2 id3 id4 count1 count2 S1001 450 GAF ARHGAP18 1.56E-05 1483 S1001 450 GAF ARHGAP12 5E-05 3698 ...
rna-seq written 4 days ago by David_emir310 • updated 4 days ago by Devon Ryan87k
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Downloading RNA-Seq Raw Count data form ICGC
... Hi All, I am looking for downloading Raw-counts for PAAD from RNA-seq data From ICGC portal. Is there a way where we can download data in matrix form? Please let me know. Thanks in Advance, Regards, DaV. ...
icgc raw_data rna-seq written 5 days ago by David_emir310
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Comment: C: Does TCGA data represents whole population
... Hi Ram Thanks for the reply, maybe not that much to change into new species. But there will be some changes, some mutations, which might be commonly not seen in native populations because of so many reasons like Environment, Diet change, etc. I might be wrong but This thought in me is pricking from ...
written 5 weeks ago by David_emir310
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Comment: C: Does TCGA data represents whole population
... Thanks a lot, Kevin, one quick question, can we treat Diaspora on par with Native Population? I mean, if 2nd generations Indians/Asians(Who were born in the US) staying in the US for a very long time then can we treat them alike? Thanks a lot, Kevin. ...
written 5 weeks ago by David_emir310
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Does TCGA data represents whole population
... Hi, I am working on TCGA Datasets and have few questions regarding this. My work is mainly involved around identifying genes which are disease-causing, i.e directly or by secondary activation. going forward, I have few doubts and need your opinion on the following 1. Can TCGA datasets be used to p ...
tcga written 5 weeks ago by David_emir310

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