User: brianj.park

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brianj.park50
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Montréal, Canada
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3 years, 2 months ago
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Posts by brianj.park

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Comparing gene ontology for two lists of genes
... You could give clusterProfiler a shot using `compareCluster()`. You'd need to prepare a data frame where each column is a gene list and then do something like: require(clusterProfiler) require(enrichplot) require(org.Hs.eg.db) cluster <- compareCluster(geneClusters = df, fun = " ...
written 7 weeks ago by brianj.park50
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Answer: A: Differential gene expression help
... Your design matrix made with `model.matrix()` needs to have the same number of rows as the columns in your count table (i.e., the number of your samples). It'd help if you posted your code and examples. ...
written 8 weeks ago by brianj.park50
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Answer: A: Bioinformatics: Converting Protein Refseq ID to Entrez Gene Accession
... You can use [org.Mm.eg.db][1]. library(org.Mm.eg.db) Mm <- org.Mm.eg.db my_symbol <- "NP_001229937" select(mm, keys = my_symbol, columns = c("REFSEQ", "ENSEMBL"), keytype = "REFSEQ") REFSEQ ENSEMBL 1 NP_001229937 ENSMUSG00000048126 [1]: https://bioc ...
written 3 months ago by brianj.park50
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Comment: C: small RNA seq data from human cell line only give me 0 counts
... is there a chance you entered the wrong strand orientation for your reads? Specifically it's the `--stranded` option when you run htseq-count. ...
written 3 months ago by brianj.park50
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Comment: C: Compare sets of GO enrichments
... Do you mean you want a database of gene sets? Above graph is using Gene Ontology (GO) database to associate related genes by their function (i.e., BP, MF, CC). http://geneontology.org/ You may also use KEGG which is divided into 7 broad categories of biochemical processes: https://www.genome.jp/keg ...
written 3 months ago by brianj.park50
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Comment: C: Compare sets of GO enrichments
... You need a data frame in which the columns correspond to a list of gene identifiers. Check the vignette for clusterProfiler, specifically chapter 11. https://yulab-smu.github.io/clusterProfiler-book/chapter11.html ...
written 3 months ago by brianj.park50
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Answer: A: ERROR: failed to find the gene identifier attribute in the 9th column of the pro
... Have you looked at the contents of your provided GTF file? With the `-g` option on featureCounts you're telling it to look for the identifier you proided. Most likely your GTF file is either missing the identifier you provided or is using a different name. ...
written 3 months ago by brianj.park50
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Answer: A: RNA_Seq Data Analyse
... After you imported your count table into R, you have to create a DGEList object that contains your counts, gene IDs, and sample group info needed for differential expression. Follow [this vigenette][1] and it should be straightforward. [1]: https://bioconductor.org/packages/release/workflows/v ...
written 5 months ago by brianj.park50
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Answer: A: Downstream RNA seq analysis
... You could take the list of differentially expressed genes and their p-values to do some gene ontology enrichment analysis. [TopGO][1] is a useful tool on R for that. [1]: https://bioconductor.org/packages/release/bioc/html/topGO.html ...
written 5 months ago by brianj.park50
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Answer: A: How to correctly generate alignment Stat in RNA-Seq
... Check [RSeQC:][1] in particular `bam_stat.py` [1]: http://rseqc.sourceforge.net/#bam-stat-py ...
written 5 months ago by brianj.park50

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Scholar 6 weeks ago, created an answer that has been accepted. For A: Comparing gene ontology for two lists of genes

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