User: Ramiro Magno

gravatar for Ramiro Magno
Ramiro Magno100
Reputation:
100
Status:
Trusted
Location:
CBMR, Faro, Portugal
Last seen:
4 months, 1 week ago
Joined:
2 years, 2 months ago
Email:
r***********@gmail.com

Posts by Ramiro Magno

<prev • 15 results • page 1 of 2 • next >
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Recommendation for visualizing ChIP-qPCR data?
... Just looking for an R package(s) that I could use to wrangle ChIP-qPCR data and then show it along genomic tracks? Maybe use the general-purpose ggbio? Or is there something tailored to visualizing tracks related with chromatin accessibility / epigenetic status? ...
ggbio R chip-seq histone chip-seq written 4 months ago by Ramiro Magno100
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... May the Force be with you. ...
written 12 months ago by Ramiro Magno100
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... Johannes: Thank you! Just to have an idea, how long is quite long? ...
written 12 months ago by Ramiro Magno100
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ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTablesFromEnsembl
... Hi I am trying to generate an Ensembl version 92 annotation package using the function fetchTablesFromEnsembl from the ensembldb package: fetchTablesFromEnsembl(92, species = "human") but I get this error related to missing Perl modules: Empty compile time value given to use lib at /home/rmagn ...
ensembldb written 12 months ago by Ramiro Magno100 • updated 12 months ago by Johannes Rainer1.4k
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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 17 months ago by Ramiro Magno100
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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 17 months ago by Ramiro Magno100
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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 17 months ago by Ramiro Magno100 • updated 17 months 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 18 months ago by Ramiro Magno100
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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 18 months ago by Ramiro Magno100 • updated 18 months ago by maysa_taheir50
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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 18 months ago by Ramiro Magno100

Latest awards to Ramiro Magno

Scholar 2.1 years ago, created an answer that has been accepted. For A: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
Popular Question 2.1 years ago, created a question with more than 1,000 views. For [FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Good Question 2.1 years ago, asked a question that was upvoted at least 5 times. For [FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
Appreciated 2.2 years ago, created a post with more than 5 votes. For Error in Gviz | IdeogramTrack
Student 2.2 years ago, asked a question with at least 3 up-votes. For Error in Gviz | IdeogramTrack

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