Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis24k
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Location:
National Institutes of Health, Bethesda, MD
Website:
http://watson.nci.nih....
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seandavis12
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Google Scholar Page
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Posts by Sean Davis

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Answer: C: Possible to directly compare RNA-Seq and DGE data?
... Unfortunately, probably not. ...
written 3 days ago by Sean Davis24k
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Answer: A: RNA_seq Data analysis Help - Uneven coverage of reads across gene!
... Read mapping will not be uniform across the gene, in general. The uneven coverage can be introduced in the wet lab and depends on the quality of the RNA, the isolation and extraction of the RNA, the library preparation strategy, and other factors. Bioinformatic processing can also result in observed ...
written 4 days ago by Sean Davis24k
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Answer: A: NGS Project report formate for a Post graduate level student.
... Without really knowing the background of your project, but with knowledge that you are a grad student and, likely, in an academic setting, structuring "report" as a scientific manuscript in [IMRAD][1] format. The "format" is sufficiently general to allow flexibility, but the structure will be easily ...
written 4 days ago by Sean Davis24k
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Comment: C: Software installation error
... How are you trying to install the package? And what OS are you using? ...
written 10 days ago by Sean Davis24k
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Comment: C: Should I remove all the overrepresented sequences to improve GC content in fast
... In general, it is generally a good idea to try to figure out *why* you see the overrepresented sequences before removing them. ...
written 11 days ago by Sean Davis24k
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Answer: A: How to show all columns after performing GenomicRanges::subsetByOverlaps
... The `subsetByOverlaps` method finds the subset of the first argument that overlaps the second. It does not do a "merge" or anything like that, so columns in the first argument are the only ones returned. If you swap `gr1` and `gr2`, you'll get the subset of `gr2` that overlaps `gr1` and that will in ...
written 11 days ago by Sean Davis24k
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Answer: A: Retrieving age metadata for GEO samples
... To my knowlege, there is not any approach to query GEO to get age-related metadata without parsing text (and guessing the meaning). The Biosample database at NCBI is beginning to provide tag-value pairs for metadata, but GEO datasets are not yet includes (though SRA data are). You could give a new ...
written 13 days ago by Sean Davis24k
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Comment: C: Number of "AT" repeats in sequence greater than 500bp
... Does `letterFrequencyInSlidingView` from the Biostrings Bioconductor package do what you need to get a summary of the data? ...
written 14 days ago by Sean Davis24k
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Answer: A: Visualize nucleotides for every position in R
... library(Biostrings) fastq <- readDNAStringSet("https://d28rh4a8wq0iu5.cloudfront.net/ads1/data/ERR037900_1.first1000.fastq","fastq") freq <- alphabetFrequency(fastq, as.prob = T,baseOnly=T) matplot(freq,type='l') legend(legend = colnames(freq),x=700,y=0.7,lty=1:5,col=1:5) ...
written 15 days ago by Sean Davis24k
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Comment: C: Protocol To Downlad TCGA Data From GDC
... The gdc-client is a command-line tool. You cannot just double-click on it. See https://docs.gdc.cancer.gov/Data_Transfer_Tool/Users_Guide/Data_Download_and_Upload/. If you have other problems, feel free to contact the gdc support staff: support@nci-gdc.datacommons.io. ...
written 15 days ago by Sean Davis24k

Latest awards to Sean Davis

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: What Figure You Make For Qc Of Whole Exome Sequencing Data
Scholar 15 days ago, created an answer that has been accepted. For C: how to cluster genes in heatmap
Scholar 18 days ago, created an answer that has been accepted. For C: how to cluster genes in heatmap
Scholar 18 days ago, created an answer that has been accepted. For A: SPLIT AND DISCORDANT READS
Scholar 27 days ago, created an answer that has been accepted. For A: Salmon unmapped reads
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: How To Get Promoter Sequences For Human Genes?
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to get FASTQ files for diseased and receptive normal samples from TCGA datab
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Clients to access TCGA data from R and Python
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Add A Unique Identifier For Fasta File To A Long List Of Sequences
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Going For The Right P-Value With Limma
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Organize A Pipeline Of Small Scripts Together?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Get Promoter Sequences For Human Genes?
Popular Question 4 months ago, created a question with more than 1,000 views. For Quick four-question survey on bioinformatics postdoc career path
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Per
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: How To Add A Unique Identifier For Fasta File To A Long List Of Sequences
Appreciated 4 months ago, created a post with more than 5 votes. For Introduction To R Course Materials Available
Appreciated 4 months ago, created a post with more than 5 votes. For Bioconductor 2015 conference live tweeting and materials
Appreciated 4 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
Appreciated 6 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
Appreciated 8 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: How To Download All Sra Samples At Once ?
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Csv File Parsing With Perl
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Where Should I Start From ?
Popular Question 8 months ago, created a question with more than 1,000 views. For Quick four-question survey on bioinformatics postdoc career path

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