User: Brian Smith

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Brian Smith120
Reputation:
120
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Trusted
Location:
United States
Last seen:
1 month, 1 week ago
Joined:
5 years, 10 months ago
Email:
b***********@gmail.com

Posts by Brian Smith

<prev • 55 results • page 1 of 6 • next >
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TxDb basic question
... Hi, I was exploring the rhesus macaque package: > TxDb.Mmulatta.UCSC.rheMac8.refGene TxDb object: # Db type: TxDb # Supporting package: GenomicFeatures # Data source: UCSC rheMac8 refGene # Organism: Macaca mulatta # Taxonomy ID: 9544 # miRBase build ID: NA # Genome: NA # transcript_nrow: 6378 ...
txdb txdb.mmulatta.ucsc.rhemac8.refgene written 14 months ago by Brian Smith120 • updated 13 months ago by daniel.vantwisk50
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Comment: C: Biostrings: "Error in .normargSEW(start, "start")"
... D'oh..!! Thanks!! ...
written 14 months ago by Brian Smith120
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Biostrings: "Error in .normargSEW(start, "start")"
... Hi, I was getting an error with a simple Biostring function. Here is the code, error and session info. Am I using some outdated package? many thanks! ====================== > library(Biostrings) > > tdna <- DNAString("TGCGATGCGCACG") > print(tdna) 13-letter "DNAString" instanc ...
biostrings written 14 months ago by Brian Smith120 • updated 14 months ago by Martin Morgan ♦♦ 23k
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genes in rhesus genome (ref. TxDb.Mmulatta.UCSC.rheMac8.refGene)
... Hi, I was trying to do some comparative analysis between the rhesus and human genes. I seem to get no genes that are common to both species! What am I doing wrong? My code, screen output :   ============= library("TxDb.Hsapiens.UCSC.hg38.knownGene") library("org.Hs.eg.db") library("TxDb.Mmulatt ...
org.hs.eg.db org.mmu.eg.db written 16 months ago by Brian Smith120 • updated 16 months ago by James W. MacDonald50k
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Comment: C: RNA-Seq : zero counts
... Thanks thokall. You were right! ...
written 20 months ago by Brian Smith120
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Comment: C: RNA-Seq : zero counts
... ah, I now see what the error message was trying to tell me! James, thanks for all your help!! ...
written 20 months ago by Brian Smith120
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Comment: C: RNA-Seq : zero counts
... Hi James, Thanks for the reply. Yep, you were right - checking back, it was aligned using UCSC while I was trying with ensembl.  As per your suggestion above, I tried using UCSC but get a new error:   > ebg <- exonsBy(TxDb.Hsapiens.UCSC.hg38.knownGene, by="gene") > bamfiles <- BamFi ...
written 20 months ago by Brian Smith120
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RNA-Seq : zero counts
... Hi, This is my first time with RNA-Seq analysis, so I might be doing something wrong! I got some bam files from a collaborator that I need to process. I followed the pipeline, but I seem to be getting 0 counts! The warnings given are "The 2 combined objects have no sequence levels in common." What ...
rnaseq bioconductor written 21 months ago by Brian Smith120 • updated 21 months ago by James W. MacDonald50k
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Epigenetic clock (Horvath): package?
... Hi, I was working with some illumina EPIC data and trying to determine the epigenetic age of samples for whole blood. I know that on Horvath's website there is an online calculator for whole blood, but the code doesn't seem to be provided. Also, in the vignette for minfi, in section "Other stuff" t ...
epigenetics minfi methylation illimina 450k methylation written 2.6 years ago by Brian Smith120 • updated 2.5 years ago by Wade Davis60
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Answer: A: SAM/siggenes: Differential gene expression analysis
... Thanks James! ...
written 2.6 years ago by Brian Smith120

Latest awards to Brian Smith

Popular Question 13 months ago, created a question with more than 1,000 views. For IlluminaHumanMethylation450k.db - error on trying to insall
Popular Question 13 months ago, created a question with more than 1,000 views. For DMRcate: incorporating covariates to find DMRs in methylation data?
Popular Question 13 months ago, created a question with more than 1,000 views. For Chromosome position to nucleotide - Biostrings?
Popular Question 13 months ago, created a question with more than 1,000 views. For org.Hs.eg.db - hg38 build?
Popular Question 13 months ago, created a question with more than 1,000 views. For IlluminaHumanMethylation450k.db - error on trying to insall
Great Question 13 months ago, created a question with more than 5,000 views. For BiomaRt: protein coding transcript identification
Popular Question 13 months ago, created a question with more than 1,000 views. For minfi: error with estimateCellCounts
Popular Question 13 months ago, created a question with more than 1,000 views. For RnBeads - doesn't produce pdfs
Popular Question 16 months ago, created a question with more than 1,000 views. For IlluminaHumanMethylation450k.db - error on trying to insall
Student 2.5 years ago, asked a question with at least 3 up-votes. For Chromosome position to nucleotide - Biostrings?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For topGO: genes annotated to a significant GO term
Popular Question 2.5 years ago, created a question with more than 1,000 views. For org.Hs.eg.db - convert ALIAS to ENTREZID, GENENAME
Popular Question 2.5 years ago, created a question with more than 1,000 views. For BiomaRt: protein coding transcript identification
Popular Question 3.5 years ago, created a question with more than 1,000 views. For BiomaRt: protein coding transcript identification
Popular Question 3.5 years ago, created a question with more than 1,000 views. For topGO: How to create gene2GO annotation for mouse?

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