Moderator: Levi Waldron

gravatar for Levi Waldron
Levi Waldron690
Reputation:
690
Status:
Trusted
Location:
CUNY Graduate School of Public Health and Health Policy, New York, NY
Website:
http://www.waldronlab.io/
Twitter:
leviwaldron1
Scholar ID:
Google Scholar Page
Last seen:
6 days, 13 hours ago
Joined:
9 years, 4 months ago
Email:
l****************@gmail.com

I'm an assistant professor of biostatistics at the CUNY Graduate School of Public Health and Health Policy in New York City, and have a special interest in streamlining the analysis of publicly available cancer genomics data in Bioconductor.  I maintain the curatedOvarianData, ffpe, and ffpeExampleData Bioconductor packages, and was closely involved with the creation of curatedCRCData, curatedBladderData, and simulatorZ.  I also maintain a couple CRAN packages: HGNChelper and pensim.  I'm involved in the development of curated data resources and methods for the analysis of multi-assay genomic experiments such as TCGA in Bioconductor (https://github.com/waldronlab/biocMultiAssay).

Posts by Levi Waldron

<prev • 83 results • page 1 of 9 • next >
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Comment: C: MultiAssayExperiment: how can i change name of a experiment in a multiassayexper
... You would have to use the development version of Bioconductor to get this update before the next release (which will happen in October): http://bioconductor.org/developers/how-to/useDevel/ ...
written 10 days ago by Levi Waldron690
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Comment: C: MultiAssayExperiment: how can i change name of a experiment in a multiassayexper
... That's great, Marcel. Nice feature addition.  ...
written 12 days ago by Levi Waldron690
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Comment: C: MultiAssayExperiment: how can i change name of a experiment in a multiassayexper
... Marcel has provided the real solution to your request below - thanks for the feature request! But if you are using bioc-release and just want a hack in the meantime, here it is. The error you saw was due to trying to subset to an experiment that doesn't exist, it isn't related to wideFormat(). See t ...
written 12 days ago by Levi Waldron690
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Comment: C: MultiAssayExperiment: how can i change name of a experiment in a multiassayexper
... > > when i try to generate wideFormat: > > > wideFormat(mae2[ , , c("exp_3")] > > Error: subscript contains invalid rownames > > Any idea? > I don't think you have renamed the experiment, and you don't have one named exp_3. I'm not at a computer but will give a more com ...
written 13 days ago by Levi Waldron690
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Answer: A: MultiAssayExperiment: how can i change name of a experiment in a multiassayexper
... There's currently no direct way to rename an ExperimentList slot, because the sampleMap would have to be modified simultaneously. One hack would be to use the `c()` function to concatenate a new ExperimentList element, then subset to remove the old one. I'm not sure if this is a common enough use ca ...
written 13 days ago by Levi Waldron690
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Comment: C: Metaphlan2 marker database used by curatedMetagenomicData
... - You're right about viruses not being included in the phylogenetic tree. That's because it was generated by PhyloPhlAn: microbial Tree of Life using 400 universal proteins (bacterial and archaeal proteins, that is): https://bitbucket.org/nsegata/phylophlan/wiki/Home. More generally, although I'm no ...
written 15 days ago by Levi Waldron690
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Comment: C: Metaphlan2 marker database used by curatedMetagenomicData
... I can add that I've confirmed there have been no changes to the metaphlan2 database since what was used to generate curatedMetagenomicData. We'll do a complete update after Metaphlan3 is released in the coming months. ...
written 15 days ago by Levi Waldron690
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Answer: A: Metaphlan2 marker database used by curatedMetagenomicData
... We used MetaPhlAn 2.0, with ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic). Note that each dataset shows only clades that were present in at least one specimen - are you sure that the species you are looking for is not present in any dataset in curatedM ...
written 16 days ago by Levi Waldron690
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Comment: C: TCGA biolinks - Samples with multiple profiles
... One more note, TCGAutils also provides simplified utilities for mapping barcode <--> UUID and UUID <--> UUID, including: UUIDtoBarcode(id_vector, id_type = c("case_id", "file_id"), end_point = "participant", legacy = FALSE) UUIDtoUUID(id_vector, to_type = c("case_id", "file_id"), legacy ...
written 26 days ago by Levi Waldron690
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Comment: C: TCGA biolinks - Samples with multiple profiles
... I'm not sure if this will be helpful to you, but the "sampleMap" files in ExperimentHub (created for use by curatedTCGAData) contain the aliquot and case barcodes, and the TCGAutils package provides a utility for filtering by sample type. There's a warning in the example below because some barcodes ...
written 26 days ago by Levi Waldron690

Latest awards to Levi Waldron

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Reproducibility of MultiDataSet Comparison
Popular Question 3 months ago, created a question with more than 1,000 views. For multiple ColSideColors-type annotations on a heatmap
Scholar 3 months ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Supporter 3 months ago, voted at least 25 times.
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Scholar 5 months ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Reproducibility of MultiDataSet Comparison
Popular Question 2.4 years ago, created a question with more than 1,000 views. For multiple ColSideColors-type annotations on a heatmap
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Scholar 3.8 years ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Autobiographer 3.9 years ago, has more than 80 characters in the information field of the user's profile.

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