User: Ramiro Magno

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Ramiro Magno80
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80
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Location:
CBMR, Faro, Portugal
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1 week, 4 days ago
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9 months, 1 week ago
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r***********@gmail.com

Posts by Ramiro Magno

<prev • 11 results • page 1 of 2 • next >
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Comment: C: How to construct an up-to-date and annotation-rich RangeSummarizedExperiment obj
... Thank you for your answer Sean. Do you see any problem in using this approach: 1. Fetch the EST sequences corresponding to the microarray probe IDs using genbankr pkg? 2. Use gmapR pkg and the human genome BSgenome.Hsapiens.NCBI.GRCh38 to map the sequences. 3. Convert the `GAlignments` objects o ...
written 15 days ago by Ramiro Magno80
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Comment: C: update TCGAbiolinks to version 3.6 and GDCquery doesn't work
... could this be a duplicate? https://support.bioconductor.org/p/102119/ ...
written 15 days ago by Ramiro Magno80
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How to construct an up-to-date and annotation-rich RangeSummarizedExperiment object around old microarray data?
... Hi All, I would like to construct a RangedSummarizedExperiment from an ExpressionSet (eSet) object (microarray data). I can get an eSet from GEO just fine: perou2000_gse <- getGEO("GSE61", destdir = inputdatapath, GSEMatrix=TRUE) perou2000_eset@annotation # returns "GPL180" and I can get b ...
geoquery summarizedexperiment rangedsummarizedexperiment written 15 days ago by Ramiro Magno80 • updated 15 days ago by Sean Davis21k
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Comment: C: TCGAbiolinks GDCquery Error: Parsing problems
... It seems the problem is in the function getGDCprojects in file R/internal.R. Simplifying the code in getGDCprojects to download json only seems to solve the issue: #' @title Retrieve all GDC projects #' @description #' getGDCprojects uses the following api to get projects #' https://gdc-api.n ...
written 26 days ago by Ramiro Magno80
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TCGAbiolinks GDCquery Error: Parsing problems
... Using TCGAbiolinks 2.5.9. It seems that the GDC API might have changed something because GDCquery("TCGA-BRCA") Returns: o GDCquery: Searching in GDC database Genome of reference: hg38 Warning: 40 parsing failures. row # A tibble: 5 x 5 col row col expected actual file expected actual 1 1 8 c ...
tcgabiolinks written 28 days ago by Ramiro Magno80 • updated 24 days ago by maysa_taheir30
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Answer: A: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
... My apologies... read.maf expects a tab-delimited file and the downloaded MAF file with TCGAbiolinks is CSV. ...
written 6 weeks ago by Ramiro Magno80
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maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
... Hi All, I have downloaded a Maf file using TCGAbiolinks (version 2.5.9): maf <- GDCquery_Maf("BRCA", pipelines = "muse", save.csv = TRUE) Then I tried to load it as a Maf object using the maftools package (version 1.2.30): BRCA_maf_csv <- "GDCdata/TCGA.BRCA.muse.d9876b23-3e7d-4d7b-bc1b-3b ...
software error tcgabiolinks maftools written 6 weeks ago by Ramiro Magno80 • updated 23 days ago by tiagochst90
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Comment: C: How often are SNPlocs.Hsapiens.dbSNP-* packages released? and why that time scal
... Hi Hervé, Thanks anyways. I am going to install R devel and your recent SNPlocs package. RM ...
written 9 months ago by Ramiro Magno80
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Comment: C: How often are SNPlocs.Hsapiens.dbSNP-* packages released? and why that time scal
... Thank you for your quick reply. May I ask another thing? For each dbSNP build, NCBI provides this file RsMergeArch.bcp.gz that contains a translation table for SNPs that have been merged to new rsIDs. Is this type of resolution taken into account in SNPlocs.Hsapiens.dbSNP149.GRCh38, or do I need to ...
written 9 months ago by Ramiro Magno80
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How often are SNPlocs.Hsapiens.dbSNP-* packages released? and why that time scale?
... I am interested in accessing SNP annotation from dbSNP using a package like SNPlocs.Hsapiens.dbSNP-*. It seems however that these packages are not updated for every dbSNP build.  Why are these pkgs not built more often? If I wanted to build a SNPlocs.Hsapiens.dbSNP-* package for the most recent ...
snp snplocs dbsnp written 9 months ago by Ramiro Magno80

Latest awards to Ramiro Magno

Popular Question 8 months ago, created a question with more than 1,000 views. For [FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Good Question 8 months ago, asked a question that was upvoted at least 5 times. For [FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Appreciated 9 months ago, created a post with more than 5 votes. For Error in Gviz | IdeogramTrack
Student 9 months ago, asked a question with at least 3 up-votes. For Error in Gviz | IdeogramTrack

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