Moderator: Sean Davis
Sean Davis ♦ 21k
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- http://watson.nci.nih....
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Posts by Sean Davis
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... 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 5 weeks ago by
Sean Davis ♦ 21k
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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 10 weeks ago by
Sean Davis ♦ 21k
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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 10 weeks ago by
Sean Davis ♦ 21k
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... Thanks, Martin, for completing the thought!
...
written 4 months ago by
Sean Davis ♦ 21k
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... 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 4 months ago by
Sean Davis ♦ 21k
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... 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 4 months ago by
Sean Davis ♦ 21k
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... 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 4 months ago by
Sean Davis ♦ 21k
• updated 4 months ago by
Martin Morgan ♦♦ 22k
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... 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 4 months ago by
Sean Davis ♦ 21k
0
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... 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 4 months ago by
Sean Davis ♦ 21k
0
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129
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... Looks like this submission contains no processed data from the submitter.
...
written 4 months ago by
Sean Davis ♦ 21k
Latest awards to Sean Davis
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12 weeks ago,
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For Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
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16 months ago,
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For Bioconductor packages now each have a DOI.
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16 months ago,
created a post with more than 5 votes.
For Invitation to submit articles to the Bioconductor gateway on F1000Research
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16 months ago,
created a post with more than 5 votes.
For Accessing Public Genomic Data from Bioconductor
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For Illumina Expression analysis from iDAT files
Guru
16 months ago,
received more than 100 upvotes.
Scholar
16 months ago,
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For A: SummarizedExperiment object from GEOquery obtained GSE
Scholar
16 months ago,
created an answer that has been accepted.
For A: Are two biological replicates enough for a transcriptome analysis using DESeq2?
Scholar
16 months ago,
created an answer that has been accepted.
For A: GEOquery Fails to Download Series Matrix File
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16 months ago,
created an answer that has been accepted.
For A: getGEO Error: Duplicate identifiers for rows
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created an answer that has been accepted.
For C: getGEO error when trying to download a series matrix file
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16 months ago,
created an answer that has been accepted.
For A: SRAdb: could not find function "sqliteTableFields"
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: SummarizedExperiment object from GEOquery obtained GSE
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: Adding a column to phenoData dataframe
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: GEOquery Fails to Download Series Matrix File
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: GEOquery: 0 features in the gset object
Teacher
16 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?
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: GEOquery Fails to Download Series Matrix File
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2.3 years ago,
created a question with more than 1,000 views.
For Accessing Public Genomic Data from Bioconductor
Scholar
2.3 years ago,
created an answer that has been accepted.
For A: GEOquery Fails to Download Series Matrix File
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2.3 years ago,
created a question with more than 1,000 views.
For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For Illumina Expression analysis from iDAT files
Appreciated
2.3 years ago,
created a post with more than 5 votes.
For Bootstrap confidence intervals on RNA-seq expression from Kallisto
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2.3 years ago,
created a question with more than 1,000 views.
For Accessing Public Genomic Data from Bioconductor
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Illumina Expression analysis from iDAT files
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