The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Moderator: Levi Waldron

gravatar for Levi Waldron
Levi Waldron840
Reputation:
840
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:
22 hours ago
Joined:
9 years, 9 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 • 90 results • page 2 of 9 • next >
0
votes
2
answers
235
views
2
answers
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 5 months ago by Levi Waldron840
1
vote
2
answers
235
views
2
answers
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 5 months ago by Levi Waldron840
0
votes
1
answer
231
views
1
answers
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 5 months ago by Levi Waldron840
0
votes
1
answer
231
views
1
answers
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 5 months ago by Levi Waldron840
1
vote
1
answer
231
views
1
answers
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 5 months ago by Levi Waldron840
1
vote
0
answers
289
views
0
answers
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 5 months ago by Levi Waldron840
1
vote
0
answers
289
views
0
answers
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 5 months ago by Levi Waldron840
3
votes
1
answer
167
views
1
answer
Simplifying a RaggedExperiment using qreduceAssay and weighted means.
... The qreduceAssay() example from the RaggedExperiment vignette demonstrates reducing multiple ranges using a weightedmean function, but there are not actually any ranges requiring weighted means: library(GenomicRanges) library(RaggedExperiment) sample1 <- GRanges( c(A = "chr1:1-10:-", B = "chr ...
genomicranges raggedexperiment written 7 months ago by Levi Waldron840 • updated 7 months ago by Martin Morgan ♦♦ 22k
2
votes
4
answers
284
views
4
answers
Comment: C: MultiAssayExperiment: how to store data for multiple cancer lesions for each pat
... colData would be something like: | | PatientID | vital_status | lesion | |----------------|------------------|--------------|---------| | TCGA-A1-A0SB.1 | TCGA-A1-A0SB | 7 | primary | | TCGA-A1-A0SB.2 | TCGA-A1-A0SB | 7 | mets | | TCGA-A1-A0S ...
written 7 months ago by Levi Waldron840
0
votes
4
answers
284
views
4
answers
Comment: C: MultiAssayExperiment: how to store data for multiple cancer lesions for each pat
... Giving up on Markdown, here is the text colData:   | | biopsy | lesion | |------|--------|--------| | HCA | 1 | HCA | | HCB | 1 | HCB |   ...
written 7 months ago by Levi Waldron840

Latest awards to Levi Waldron

Popular Question 4 months ago, created a question with more than 1,000 views. For Error creating DESeqDataSet from "airway" SummarizedExperiment
Appreciated 4 months ago, created a post with more than 5 votes. For BioC2019 June 24-27 in New York City
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Reproducibility of MultiDataSet Comparison
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Supporter 8 months ago, voted at least 25 times.
Scholar 8 months ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For multiple ColSideColors-type annotations on a heatmap
Scholar 10 months ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Reproducibility of MultiDataSet Comparison
Popular Question 2.9 years ago, created a question with more than 1,000 views. For multiple ColSideColors-type annotations on a heatmap
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Scholar 4.2 years ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Autobiographer 4.3 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 389 users visited in the last hour