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:
1 week, 1 day 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 2 of 9 • next >
3
votes
1
answer
88
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 10 weeks ago by Levi Waldron690 • updated 10 weeks ago by Martin Morgan ♦♦ 22k
0
votes
4
answers
157
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 12 weeks ago by Levi Waldron690
0
votes
4
answers
157
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 12 weeks ago by Levi Waldron690
0
votes
4
answers
157
views
4
answers
Comment: C: MultiAssayExperiment: how to store data for multiple cancer lesions for each pat
... Seem to be having some Markdown issues. The colData table was intended to be: | | biopsy | lesion | |------|--------|--------| | HCA | 1 | HCA | | HCB | 1 | HCB | ...
written 12 weeks ago by Levi Waldron690
0
votes
4
answers
157
views
4
answers
Comment: C: MultiAssayExperiment: how to store data for multiple cancer lesions for each pat
... This would be your MultiAssayExperiment colData (where HCA and HCB in the rownames would be replaced by unique identifiers if you repeat HCA and HCB as lesion identifiers in multiple biopsies. biopsy lesion HCA 1 HCA HCB 1 HCB And the MultiAssayExperiment sampleMap would look like this ...
written 12 weeks ago by Levi Waldron690
0
votes
1
answers
72
views
1
answers
Answer: A: Horizontal integration of multi omic data, with continuous dependent variable
... I'm not totally clear on what your goal is, but it sounds possibly you want to do regression on a continuous dependent variable. If that's the case, you might check out: mlR: https://mlr-org.github.io/mlr-tutorial/devel/html/create_learner/index.html#regression caret: https://www.machinelearningplu ...
written 12 weeks ago by Levi Waldron690
0
votes
4
answers
157
views
4
answers
Answer: A: MultiAssayExperiment: how to store data for multiple cancer lesions for each pat
... Dear Mario, I'm not sure I understand your question yet. It sounds like you have already stored these two SummarizedExperiment objects in a MultiAssayExperiment? Are you unable to access or manipulate the data in the way you want in the way you've constructed your MultiAssayExperiment, and if so, wh ...
written 12 weeks ago by Levi Waldron690
0
votes
1
answers
118
views
1
answers
Comment: C: Querying specific TCGA datasets through the MultiAssayExperiment R package
... They're based on the Firehose output, which says in its FAQ that: Q: What reference genome build are you using? A: We match the reference genome used in our analyses to the reference used to generate the data as appropriate. Our understanding is that TCGA standards stipulate that OV, COAD/READ, an ...
written 12 weeks ago by Levi Waldron690
0
votes
1
answers
88
views
1
answers
Answer: A: MultiAssayExperiment wideformat operations
... The answer to your first question is a little hidden in the longFormat section of ?MultiAssayExperiment-helpers: longFormat(object, colDataCols = NULL, i = 1L) wideFormat(object, colDataCols = NULL, check.names = TRUE, collapse = "_", i = 1L) longFormat The longFormat method takes data from the Expe ...
written 3 months ago by Levi Waldron690
0
votes
1
answers
104
views
1
answers
Answer: A: subsets different type of data together
... Yes. If you subset by GRanges, all rows of the SummarizedExperiment will be dropped. But subsetting by rownames will act consistently on both. ...
written 3 months 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.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 134 users visited in the last hour