Moderator: Sean Davis

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Sean Davis21k
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http://watson.nci.nih....
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@seandavis12
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Posts by Sean Davis

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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 7 days 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 7 days 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 7 days 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 7 days ago by Sean Davis21k • updated 7 days ago by Martin Morgan ♦♦ 21k
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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 14 days 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 14 days 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 14 days ago by Sean Davis21k
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Comment: C: Invitation to submit articles to the Bioconductor gateway on F1000Research
... 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 Davis21k
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News: Invitation to submit articles to the Bioconductor gateway on F1000Research
... 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 ...
news publication written 26 days ago by Sean Davis21k
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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 Davis21k

Latest awards to Sean Davis

Teacher 13 months ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Scholar 2.0 years ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Appreciated 2.0 years ago, created a post with more than 5 votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 2.0 years ago, created a question with more than 1,000 views. For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Teacher 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
Scholar 2.2 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
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Appreciated 2.5 years ago, created a post with more than 5 votes. For Bioc2015 conference ongoing now.
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: differential gene expression
Student 2.9 years ago, asked a question with at least 3 up-votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Scholar 3.2 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Scholar 3.2 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
Supporter 3.2 years ago, voted at least 25 times.
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: differential gene expression
Scholar 3.5 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Scholar 3.5 years ago, created an answer that has been accepted. For A: Processing RAW CEL files from GEO
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
Oracle 3.6 years ago, created more than 1,000 posts (questions + answers + comments).
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