User: K

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K50
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50
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Posts by K

<prev • 48 results • page 1 of 5 • next >
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Comment: C: Looking for Batch effects in PCA
... Thank you for the feedback. I did infact use EdgeR for differential expression analysis of this data, and we got an unusually extremely large number of differentially expressed results.  That is why I'm going back to the data, and the PCA plot, to see if there is a batch effect. I need help with in ...
written 3 months ago by K50
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Looking for Batch effects in PCA
... Hello, I need some advice. I'm lookin at PCA plots of RNAseq data, and am understand whether my data has batch effects or not.  I performed alignment using STAR, and then obtained gene counts, and gene TPM values I used ```prcomp``` to find the Principal components and plotted PC1 vs PC2 and PC2 v ...
batch effect pca written 3 months ago by K50
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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 9 months ago by K50 • updated 9 months ago by James W. MacDonald48k
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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 20 months ago by K50
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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 20 months ago by K50
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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 20 months ago by K50
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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 20 months ago by K50
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Answer: A: subset from fastq file
... Thank you, just realized this was such a noob question.  ...
written 2.1 years ago by K50
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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 2.1 years ago by K50
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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 2.5 years ago by K50

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Popular Question 5 months ago, created a question with more than 1,000 views. For bioconductor package for BWA-MEM ?
Popular Question 20 months ago, created a question with more than 1,000 views. For example fastq file, sampleAnnotaition and Hairpin file for shRNAseq/EdgeR tool
Popular Question 20 months ago, created a question with more than 1,000 views. For HTseq in bioconductor
Popular Question 20 months ago, created a question with more than 1,000 views. For how to download multiple gff files from NCBI
Popular Question 20 months ago, created a question with more than 1,000 views. For bioconductor package for BWA-MEM ?
Popular Question 2.7 years 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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