User: K

gravatar for K
K40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
2 weeks, 1 day ago
Joined:
2 years, 5 months ago
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k**********@gmail.com

Posts by K

<prev • 46 results • page 1 of 5 • next >
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Gene ontology enrichment
... Hello, I'm trying to replicate this Gene ontology enrichment: https://davetang.org/muse/2010/11/10/gene-ontology-enrichment-analysis/ I have been following instructions line by line. I'm at this point where I have to run the hypergeometric test. But get this error. > hgOver <- hyperGTest(pa ...
go gene ontology written 15 days ago by K40 • updated 15 days ago by James W. MacDonald45k
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Comment: C: Extracting all possible annotations between two genomic coordinates
... I believe this is it: grch37 = useEnsembl(biomart="ensembl",GRCh=37,dataset="hsapiens_gene_ensembl") ...
written 11 months ago by K40
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Comment: C: Extracting all possible annotations between two genomic coordinates
... Quick follow up question I believe using this command below, it links to the latest genome reference GrCh38. genes_mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") Could you tell me how to change setting to the GRch37 Ensembl ? ...
written 11 months ago by K40
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Answer: A: Extracting all possible annotations between two genomic coordinates
... Thank you ! This is helpful -  I will start with Biomart. That's a good start.  ...
written 11 months ago by K40
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Extracting all possible annotations between two genomic coordinates
... Hello, I have a list of several base pair locations (each have a start and end base pair). Eg: Chr:17,  BasePair1: 26804211 , BasePair2: 26818676 And I am looking to find all possible annotations including gene name, known SNPs , microRNA etc between these two base pair locations (the region need ...
genomes written 11 months ago by K40
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Answer: A: subset from fastq file
... Thank you, just realized this was such a noob question.  ...
written 16 months ago by K40
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subset from fastq file
... Hello, I am trying to extract all reads from chromosome 1 (or any other chromosome) from a fastq file. The fastq file I have is from Illumina. I looked up ShortRead package, but I don't see an example for this in the vignette.  Could someone give advice ?  Thanks, K ...
fastq written 16 months ago by K40
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Answer: A: how to get transcript annotation (unique)
... Thank you ! This is great - I will decide what to do about the duplicates.  ...
written 21 months ago by K40
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how to get transcript annotation (unique)
... Hello, I have list of transcripts (From an RNA-seq quantification output), and I would like to annotate. I would like the annotation to have the following information (Gene name, NM id or some information about the mRNA, chromosome number, chr start and end) ucscid gene mrna refs ...
txdb written 21 months ago by K40
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Answer: A: HTseq in bioconductor
... Thank you very much, I will try these out. ...
written 24 months ago by K40

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Popular Question 24 months ago, created a question with more than 1,000 views. For example fastq file, sampleAnnotaition and Hairpin file for shRNAseq/EdgeR tool

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