Moderator: Sean Davis
Sean Davis ♦ 21k
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- http://watson.nci.nih....
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- Joined:
- 9 years, 10 months ago
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Posts by Sean Davis
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170
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... Thanks, Martin, for completing the thought!
...
written 7 days ago by
Sean Davis ♦ 21k
0
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1
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170
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1
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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 7 days ago by
Sean Davis ♦ 21k
0
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1
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170
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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 7 days ago by
Sean Davis ♦ 21k
0
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1
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170
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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 7 days ago by
Sean Davis ♦ 21k
• updated 7 days ago by
Martin Morgan ♦♦ 21k
0
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52
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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 14 days ago by
Sean Davis ♦ 21k
0
votes
1
answers
52
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1
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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 14 days ago by
Sean Davis ♦ 21k
0
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1
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52
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1
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... Looks like this submission contains no processed data from the submitter.
...
written 14 days ago by
Sean Davis ♦ 21k
0
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0
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687
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0
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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 26 days ago by
Sean Davis ♦ 21k
5
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0
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687
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... We invite you to contribute to a series of articles that will accompany the BioC 2018 conference in the Bioconductor gateway on F1000Research. We are specifically looking for:
Cross-package workflows
Package-based vignettes that show how to solve a scientific problem end-to-end
Teachi ...
written 26 days ago by
Sean Davis ♦ 21k
0
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1
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70
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1
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Comment:
C: processing deseq2 result
... Hello me37uday!
It appears that your post has been cross-posted to another site: See https://www.biostars.org/p/304718/.
This is typically not recommended as it runs the risk of annoying people in both communities.
...
written 5 weeks ago by
Sean Davis ♦ 21k
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13 months ago,
created an answer with at least 3 up-votes.
For A: GEOquery Fails to Download Series Matrix File
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2.0 years ago,
created an answer that has been accepted.
For A: GEOquery Fails to Download Series Matrix File
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created a post with more than 5 votes.
For Bootstrap confidence intervals on RNA-seq expression from Kallisto
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2.0 years ago,
created a question with more than 1,000 views.
For Illumina Expression analysis from iDAT files
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created a question with more than 1,000 views.
For Accessing Public Genomic Data from Bioconductor
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created a question with more than 1,000 views.
For dplyr and the GEOmetadb package for mining NCBI GEO metadata
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2.0 years ago,
created a question with more than 1,000 views.
For Accessing Public Genomic Data from Bioconductor
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2.1 years ago,
created a question with more than 1,000 views.
For Illumina Expression analysis from iDAT files
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2.2 years ago,
created an answer with at least 3 up-votes.
For A: very high adjusted P-vals using Illumina data from GEO
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For A: SRAdb: could not find function "sqliteTableFields"
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For Bioc2015 conference ongoing now.
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For A: differential gene expression
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2.9 years ago,
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For Bootstrap confidence intervals on RNA-seq expression from Kallisto
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For A: Transitive overlaps of GRanges object
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For A: Transitive overlaps of GRanges object
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For A: differential gene expression
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For A: differential gene expression
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For A: SRAdb: could not find function "sqliteTableFields"
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3.5 years ago,
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For A: Processing RAW CEL files from GEO
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For A: differential gene expression
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