Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis21k
Reputation:
21,000
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Trusted
Location:
United States
Website:
http://watson.nci.nih....
Twitter:
@seandavis12
Scholar ID:
Google Scholar Page
Last seen:
3 weeks, 2 days ago
Joined:
10 years, 3 months ago
Email:
s*******@gmail.com

Posts by Sean Davis

<prev • 2,144 results • page 2 of 215 • next >
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Answer: A: Unable to connect to 'watson.nci.nih.gov' on port 80 using GEOmetadb R library
... We have moved the hosting of the GEOmetadb sqlite database to the more stable Amazon Web Services. Upgrading the GEOmetadb package to the most recent release should fix the issue.  ...
written 10 weeks ago by Sean Davis21k
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Comment: C: GEOquery using keywords in R
... You could either use the Bioconductor GEOmetadb package, a web interface query on the NCBI website, or eUtils. There are other third-party options as well as similar functionality at EBI. ...
written 3 months ago by Sean Davis21k
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Answer: A: GEOquery using keywords in R
... Just guessing that this is what you want: library(GEOquery) eset = getGEO('GSE73835')[[1]] eset ...
written 3 months ago by Sean Davis21k
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Comment: C: How to check the read length for all the TCGA data samples in GDC?
... Thanks, Martin, for completing the thought! ...
written 5 months ago by Sean Davis21k
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Comment: C: How to check the read length for all the TCGA data samples in GDC?
... Sure. library(dplyr) rg_info = bind_rows(z$analysis$metadata$read_groups) You may need to play with things a bit to get exactly what you want. The str() function can be quite useful, as are things like class() to see how things are stored in these complex structures. ...
written 5 months ago by Sean Davis21k
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Comment: C: How to check the read length for all the TCGA data samples in GDC?
... q = files() %>% filter(~ cases.project.project_id == 'TCGA-BRCA' & data_type == 'Aligned Reads' & experimental_strategy == 'WXS' & data_format == 'BAM') %>% select('file_id') %>% expand('analysis.metadata.read_groups') file_ids = ids(q) ...
written 5 months ago by Sean Davis21k
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Answer: A: How to check the read length for all the TCGA data samples in GDC?
... Try: library(GenomicDataCommons) # You may want to change the filter criteria, but you # get the idea.... z = files() %>% filter(~ data_format=='BAM') %>% select('file_id') %>% expand('analysis.metadata.read_groups') %>%   results() # You can view the data interactively libra ...
written 5 months ago by Sean Davis21k • updated 5 months ago by Martin Morgan ♦♦ 22k
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Comment: C: Need help loading gene expression data into R using either ArrayExpress or GEOqu
... You'll need to update R and GEOquery. That SSL error is due to a change at NCBI that has been addressed in recent GEOquery versions. As for ArrayExpress, there is no "processed" data, so that approach won't work. See my answer below. ...
written 5 months ago by Sean Davis21k
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Answer: A: Need help loading gene expression data into R using either ArrayExpress or GEOqu
... You'll need to download the supplementary files from GEO and then determine the best approach to process them. You can use the getGEOSuppFiles() function to download those raw data files. The phenoData from a getGEO() call can still be useful, though, for building out the sample information.  ...
written 5 months ago by Sean Davis21k
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Comment: C: Need help loading gene expression data into R using either ArrayExpress or GEOqu
... Looks like this submission contains no processed data from the submitter.  ...
written 5 months ago by Sean Davis21k

Latest awards to Sean Davis

Scholar 10 weeks ago, created an answer that has been accepted. For A: Filtering Gene Symbols and Sample Description from GSE files of GEO
Scholar 10 weeks ago, created an answer that has been accepted. For A: Using eset while parsing GSE file located in a path
Popular Question 4 months ago, created a question with more than 1,000 views. For Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: GEOquery: 0 features in the gset object
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to check the read length for all the TCGA data samples in GDC?
Appreciated 17 months ago, created a post with more than 5 votes. For Invitation to submit articles to the Bioconductor gateway on F1000Research
Appreciated 17 months ago, created a post with more than 5 votes. For Accessing Public Genomic Data from Bioconductor
Popular Question 17 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Guru 17 months ago, received more than 100 upvotes.
Scholar 17 months ago, created an answer that has been accepted. For A: SummarizedExperiment object from GEOquery obtained GSE
Scholar 17 months ago, created an answer that has been accepted. For A: Are two biological replicates enough for a transcriptome analysis using DESeq2?
Scholar 17 months ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Scholar 17 months ago, created an answer that has been accepted. For A: getGEO Error: Duplicate identifiers for rows
Scholar 17 months ago, created an answer that has been accepted. For C: getGEO error when trying to download a series matrix file
Scholar 17 months ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: SummarizedExperiment object from GEOquery obtained GSE
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Adding a column to phenoData dataframe
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Appreciated 17 months ago, created a post with more than 5 votes. For Bioconductor packages now each have a DOI.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Scholar 2.4 years ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Popular Question 2.4 years ago, created a question with more than 1,000 views. For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Appreciated 2.4 years ago, created a post with more than 5 votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto

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