User: Giuseppe

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Giuseppe20
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7 months, 4 weeks ago
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10 months, 4 weeks ago
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Posts by Giuseppe

<prev • 5 results • page 1 of 1 • next >
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Multiple alignment of big DNA sequences files
... Hi everybody, I have 12 fasta files of DNA sequences that I downloaded from NCBI. Every file contains ~ 30000 rows and ~2MLN of characters. I have Ubuntu 18.04 VPS with 32 GB of RAM, 8 CPUs. I want multiple alignment of sequences with "msaClustalOmega" function of the Bioconductor package msa. I e ...
genome multiplealignment written 8 months ago by Giuseppe20
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Comment: C: Download TCGA dataset like a S4 object
... thank you so much! The Only problem is that download Methylation dataset is very slow! And the S4 object occupies so much memory ...
written 9 months ago by Giuseppe20
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Comment: C: Download TCGA dataset like a S4 object
... Thank you very much for your support! I have last question.. I executed this instruction: > experiments(SKCM) ExperimentList class object of length 1: [1] SKCM_Methylation-20160128: SummarizedExperiment with 485577 rows and 475 columns I want to convert ExperimentList class to a data frame. How c ...
written 9 months ago by Giuseppe20
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Comment: C: Download TCGA dataset like a S4 object
... Thank you Mario for your answer. I want to download the following dataset : https://xenabrowser.net/datapages/?dataset=TCGA.SKCM.sampleMap%2FHiSeqV2_PANCAN&host=https%3A%2F%2Ftcga.xenahubs.net&removeHub=https%3A%2F%2Flocal.xena.ucsc.edu%3A7223&removeHub=https%3A%2F%2Fucscpublic.xenahu ...
written 9 months ago by Giuseppe20
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Download TCGA dataset like a S4 object
... Hi all, I'm making a function that uses input TCGA datasets. I know that for the purpose of reproducibility, inputs need to be BioC objects, and not text files. My question is: is there any package that allows me download TCGA datasets like a BioC objects (S4) ? Thank you so much! ...
tcga dataset written 9 months ago by Giuseppe20 • updated 9 months ago by mario.zanfardino150

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