Moderator: Sean Davis
Sean Davis ♦ 21k
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Posts by Sean Davis
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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 20 days ago by
Sean Davis ♦ 21k
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60
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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 20 days ago by
Sean Davis ♦ 21k
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256
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1
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... Thanks, Martin, for completing the thought!
...
written 9 weeks ago by
Sean Davis ♦ 21k
0
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256
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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 9 weeks 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 9 weeks 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 9 weeks ago by
Sean Davis ♦ 21k
• updated 9 weeks ago by
Martin Morgan ♦♦ 21k
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94
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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 10 weeks ago by
Sean Davis ♦ 21k
0
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94
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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 10 weeks ago by
Sean Davis ♦ 21k
0
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1
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94
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... Looks like this submission contains no processed data from the submitter.
...
written 10 weeks ago by
Sean Davis ♦ 21k
0
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999
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... I would suggest that as long as there can be some focus on how bioconductor tools facilitate the analysis, the workflow would be a nice addition.
...
written 12 weeks ago by
Sean Davis ♦ 21k
Latest awards to Sean Davis
Teacher
14 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
14 months ago,
created a post with more than 5 votes.
For Bioconductor packages now each have a DOI.
Appreciated
14 months ago,
created a post with more than 5 votes.
For Invitation to submit articles to the Bioconductor gateway on F1000Research
Appreciated
14 months ago,
created a post with more than 5 votes.
For Accessing Public Genomic Data from Bioconductor
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Illumina Expression analysis from iDAT files
Guru
14 months ago,
received more than 100 upvotes.
Scholar
14 months ago,
created an answer that has been accepted.
For A: SummarizedExperiment object from GEOquery obtained GSE
Scholar
14 months ago,
created an answer that has been accepted.
For A: Are two biological replicates enough for a transcriptome analysis using DESeq2?
Scholar
14 months ago,
created an answer that has been accepted.
For A: GEOquery Fails to Download Series Matrix File
Scholar
14 months ago,
created an answer that has been accepted.
For A: getGEO Error: Duplicate identifiers for rows
Scholar
14 months ago,
created an answer that has been accepted.
For C: getGEO error when trying to download a series matrix file
Scholar
14 months ago,
created an answer that has been accepted.
For A: SRAdb: could not find function "sqliteTableFields"
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: SummarizedExperiment object from GEOquery obtained GSE
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Adding a column to phenoData dataframe
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: GEOquery Fails to Download Series Matrix File
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: GEOquery: 0 features in the gset object
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: GEOquery Fails to Download Series Matrix File
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Accessing Public Genomic Data from Bioconductor
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: GEOquery Fails to Download Series Matrix File
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Illumina Expression analysis from iDAT files
Appreciated
2.2 years ago,
created a post with more than 5 votes.
For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Accessing Public Genomic Data from Bioconductor
Popular Question
2.2 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: SRAdb: could not find function "sqliteTableFields"
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