User: Dave Bridges

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Dave Bridges1.3k
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Posts by Dave Bridges

<prev • 48 results • page 1 of 5 • next >
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Comment: C: Using bootstrap testing in kallisto to obtain estimated transcript counts
... If the abundance estimates dont change with more bootsraps, then they only provide an estimate of technical variance?  I would have expected that they would improve (converge) as more bootstraps are done.  In other words, if the downstream algorithm isnt taking advantage of the technical variance, t ...
written 2.8 years ago by Dave Bridges1.3k
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Comment: C: Multiple Observations In Gwas Via Snps Or Exome Sequencing/Wgs
... so common variants, or non-damaging variants are filtered out pre-statistics? ...
written 4.4 years ago by Dave Bridges1.3k
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Multiple Observations In Gwas Via Snps Or Exome Sequencing/Wgs
... If you test for say 100 000 SNPs in a SNP array for some phenotype, my understanding is that you would correct for 100 000 observations. What about more in depth studies. Do people correct for all >3 million observations in whole genome sequencing (ie nucleotides in hg19), presuming there is no ...
gwas exome-sequencing snp statistics written 4.4 years ago by Dave Bridges1.3k • updated 4.4 years ago by Charles Warden5.0k
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Programmatically Obtain The Go Version From Go.Db
... I am annotating genes with GO.db but I would like to programmatically record the version/date of the gene ontology release that is used for that annotation. Is there any way to extract this from a function in GO.db. The same goes for KEGG/KEGG.db ...
R kegg go written 4.5 years ago by Dave Bridges1.3k • updated 4.1 years ago by Biostar ♦♦ 20
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Answer: A: Retrieve All Genes Associated With A Go Term
... Using biomaRt within R: library(biomaRt) ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") #uses human ensembl annotations #gets gene symbol, transcript_id and go_id for all genes annotated with GO:0007507 gene.data <- getBM(attributes=c('hgnc_symbol', 'ensembl_transcript_id', 'go_id' ...
written 5.1 years ago by Dave Bridges1.3k
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Transcription Factor Enrichment From Transcriptome
... Is there any tools to detect enrichment of transcription factor targets from microarray/RNAseq data. I have heard that Metacore has this functionality, but is there a freely available mapping of transcription factors to targets that could be queried in a way analogous to the way DAVID or GOseq quer ...
transcription-factor microarray rna-seq transcriptome written 5.2 years ago by Dave Bridges1.3k • updated 19 months ago by jin80
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Answer: A: Time Course Rna-Seq Analysis
... You should be able to use fitNbinomGLM and nbinomGLMTest from the DESeq package: library(DESeq) cds <- makeExampleCountDataSet()[ 1:100, ] cds <- estimateSizeFactors( cds ) cds <- estimateDispersions( cds, method="pooled" ) #need to use either pooled or blind time.course <- c(0,2,5,15,2 ...
written 5.2 years ago by Dave Bridges1.3k
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Comment: C: Time Course Rna-Seq Analysis
... are you testing the hypothesis that there is a non-zero change in expression (slope) or that the slopes differ over time between two groups? ...
written 5.2 years ago by Dave Bridges1.3k
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Comment: C: R: Heatmap Of Rna-Seq Count Table With Functional Gene Clustering
... Depending on how you annotate your DEseq results, you can add GO annotations (for example using biomaRt), then filter those rows for whichever GO id you are interested in. After you have the filtered dataset, the heatmap should be the same as for differentially expressed genes. ...
written 5.5 years ago by Dave Bridges1.3k
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Comment: C: How To Best Manipulate Deseq Output?
... Maybe I don't quite understand here. I thought the way described above generates a row for each exon. If an exon is in two transcripts from different, there would be two different ensemblexonids. I thought that this flattened each exon into its own counting bin and that was ok. ...
written 5.5 years ago by Dave Bridges1.3k

Latest awards to Dave Bridges

Student 2.1 years ago, asked a question with at least 3 up-votes. For What Is A Good Ontology For Experimental Results
Epic Question 2.1 years ago, created a question with more than 10,000 views. For Transcription Factor Enrichment
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Transcription Factor Enrichment From Transcriptome
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Transcription Factor Enrichment
Great Question 2.1 years ago, created a question with more than 5,000 views. For Transcription Factor Enrichment
Scholar 2.1 years ago, created an answer that has been accepted. For A: Retrieve All Genes Associated With A Go Term
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Beginners Guide To Homology Modeling
Popular Question 2.1 years ago, created a question with more than 1,000 views. For What Is A Good Ontology For Experimental Results
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Beginners Guide To Homology Modeling
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Beginners Guide To Homology Modeling
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Beginners Guide To Homology Modeling
Great Question 2.9 years ago, created a question with more than 5,000 views. For Transcription Factor Enrichment
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Beginners Guide To Homology Modeling
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Are Long Noncoding Rna (Lncrna) Included In The Ucsc Or Ensembl Genome Assemblies?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Transcription Factor Enrichment
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Number Of Samples Per Lane For Multiplexed Rna-Seq
Great Question 3.7 years ago, created a question with more than 5,000 views. For Transcription Factor Enrichment
Popular Question 3.9 years ago, created a question with more than 1,000 views. For What Is A Good Ontology For Experimental Results
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Transcription Factor Enrichment
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Are Long Noncoding Rna (Lncrna) Included In The Ucsc Or Ensembl Genome Assemblies?
Good Question 4.3 years ago, asked a question that was upvoted at least 5 times. For Transcription Factor Enrichment
Appreciated 4.3 years ago, created a post with more than 5 votes. For Database Documentation
Appreciated 4.3 years ago, created a post with more than 5 votes. For What Is The Most Appropriate Uri For A Journal Article?
Appreciated 4.3 years ago, created a post with more than 5 votes. For Transcription Factor Enrichment
Appreciated 4.3 years ago, created a post with more than 5 votes. For A: Beginners Guide To Homology Modeling

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