User: Levi Waldron

gravatar for Levi Waldron
Levi Waldron420
Reputation:
420
Status:
Trusted
Location:
CUNY Graduate School of Public Health and Health Policy, New York, NY
Website:
http://www.waldronlab....
Twitter:
leviwaldron1
Scholar ID:
Google Scholar Page
Last seen:
2 days, 10 hours ago
Joined:
9 years 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 • 53 results • page 1 of 6 • next >
0
votes
1
answers
81
views
1
answers
Comment: C: Batch Correction with only one sample in a batch
... I wouldn’t assume that because some of your “batches” include only one sample that they’re useless. I’d be interested in exploratory analysis to perform analysis of variance on the larger batches to see the relative contribution of batches and experimental factors to variance, to help understand how ...
written 2 days ago by Levi Waldron420
0
votes
1
answers
61
views
1
answers
Comment: C: Error downloading TCGA miRNA expression data
... mRNAArray3 isn't one of the allowable assay types (mRNAArray is). curatedTCGAData provides the final Firehose pipeline snapshot. While GDC provides newer processing for some assays, there are no new data. > ...
written 5 days ago by Levi Waldron420
0
votes
1
answers
61
views
1
answers
Answer: A: Error downloading TCGA miRNA expression data
... You might also try curatedTCGAData - it has an advantage of linking assays and clinical/pathological/specimen data in a MultiAssayExperiment. Here I obtain both the miRNA array and sequencing data in one MultiAssayExperiment: > library(curatedTCGAData) Loading required package: MultiAssayExperime ...
written 5 days ago by Levi Waldron420
0
votes
0
answers
66
views
0
answers
Comment: C: Eliminating repetitive calls to ExperimentHub
... `memoize` is super neat, thanks Martin. ...
written 6 days ago by Levi Waldron420
0
votes
2
answers
107
views
2
answers
Answer: A: deseq2 normalization with metagenomics data
... You might instead use Bray-Curtis beta diversity as a measure of dissimilarity, available in the phyloseq package. I could imagine differences in read depth, or a lot of low counts if there are only a couple dominant genera, resulting in low Spearman correlation even if the data are OK. ...
written 6 weeks ago by Levi Waldron420
2
votes
0
answers
86
views
0
answers
News: Bioc2018 Toronto: call for abstracts, workshop syllabi, special interest groups
... Submissions are now open at http://bioc2018.bioconductor.org/call-for-abstracts for: Call for posters and short contributed talks (submit an abstract) Call for workshops (submit a syllabus) Call for Birds of a Feather / Special Interest Groups (submit an Issue on GitHub) Deadline: ...
news bioc2018 written 10 weeks ago by Levi Waldron420
0
votes
3
answers
641
views
3
answers
Comment: C: BioC happening in 2018?
... I just stumbled across this post while googling "bioc2018" so here's the link: https://bioconductor.org/help/course-materials/2018/BioC2018/ ...
written 5 months ago by Levi Waldron420
0
votes
2
answers
233
views
2
answers
Answer: A: How to create the colData for a complex experiment
... I think I understand better now. I guess the biopsies would be labeled by intestinal location, so they are not exchangeable (for example location might be labeled stool, rectum, sigmoid, descending, transverse, ascending, caecum).  So I see several potential ways to set up: 1. separate rows in the ...
written 5 months ago by Levi Waldron420
0
votes
2
answers
233
views
2
answers
Answer: A: How to create the colData for a complex experiment
... Hi Lluís - there are different ways you could do this, but if you think of the five rows you showed of as five different "biological units", it might make sense to keep them separate in the colData as shown. The main difference from the MAE perspective will be how you interact with the object with ...
written 5 months ago by Levi Waldron420
0
votes
2
answers
297
views
2
answers
Answer: A: Reproducibility of MultiDataSet Comparison
... Also, I'm quite proud of the internal graph representation of the specimen:assay relationships (sampleMap(MAE)). It's a novel approach to maintaining consistency between specimens and any number of assays with replicates, missing data, and arbitrary per-assay naming conventions, but still have harmo ...
written 8 months ago by Levi Waldron420

Latest awards to Levi Waldron

Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Reproducibility of MultiDataSet Comparison
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
Popular Question 2.1 years ago, created a question with more than 1,000 views. For multiple ColSideColors-type annotations on a heatmap
Scholar 3.5 years ago, created an answer that has been accepted. For A: Gene set enrichment analysis
Autobiographer 3.5 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: 433 users visited in the last hour