User: Keith Hughitt

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Keith Hughitt100
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Posts by Keith Hughitt

<prev • 53 results • page 1 of 6 • next >
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Comment: C: Unexpected format to the list of available marts error (12/11/2017)
... I can confirm the present server issues. Below, for example, the first two requests below succeed and the later two fail: > useMart(biomart='ensembl', dataset='hsapiens_gene_ensembl', host='www.ensembl.org') Object of class 'Mart': Using the ENSEMBL_MART_ENSEMBL BioMart database Using the ...
written 10 weeks ago by Keith Hughitt100
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Answer: A: Finding orthologous human/mouse ENSEMBL IDs
... In case it helps anyone else, I was able to solve this using the second method suggested in the earlier post -- biomaRt's "getLDS()" function: mart1 = useMart("ensembl", dataset="hsapiens_gene_ensembl") mart2 = useMart("ensembl", dataset="mmusculus_gene_ensembl") human_ids <- c('E ...
written 8 months ago by Keith Hughitt100
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Finding orthologous human/mouse ENSEMBL IDs
... Greetings, I was wondering if someone might be able to help suggest a good way to generate a mapping of human/mouse orthologs, using ENSEMBL gene IDs? I found a very old post which pointed me to the inpIDMapper function in the AnntoationDbi package. The example usage shows how this function can be ...
annotationdbi ensembl human mouse homologue written 8 months ago by Keith Hughitt100
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Comment: C: rtracklayer import.gff3 function no longer working in R 3.4
... Indeed it does! downgrade with biocLite(c("ExpressionAtlas", "GenomeInfoDb", "OrganismDbi", "knitcitations")) Error: 288 package(s) out of date; 4 package(s) too new In the past, I would just use "biocLite()" to see which packages were out-of-date, but that was not returning anything in this c ...
written 10 months ago by Keith Hughitt100
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Comment: C: rtracklayer import.gff3 function no longer working in R 3.4
... Good catch! It looks like the "3.4" directory may have been previously used by the SVN version of of R, and some newer packages got mixed in. Martin's suggestion below further supports this. Thanks for the insight! ...
written 10 months ago by Keith Hughitt100
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rtracklayer import.gff3 function no longer working in R 3.4
... After upgrading to R 3.4/Bioconductor 3.4 today, the `import.gff3` function (and presumably other related functions) are no longer working for me. For example, using this sample GFF3 file from ENSEMBL, with spaces replaced with tabs: ##gff-version 3 ctg123 . mRNA 1300 9000 . ...
rtracklayer gff import.gff3 written 10 months ago by Keith Hughitt100 • updated 10 months ago by Martin Morgan ♦♦ 21k
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Using readAAMultipleAlignment to parse CMFinder Stockholm format alignments
... Greetings, I'm currently working on a pipeline which makes use of the downloadable version of the covariance model-based RNA motif detection program, CMFinder. CMFinder outputs detected motifs in a modified version of the Stockholm output format. (Example: http://bio.cs.washington.edu/CMfinder/glm ...
biostrings msa stockholm cmfinder written 13 months ago by Keith Hughitt100
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Comment: C: ArrayExpress unable to find raw data: "Experiment has no raw files available"
... Thanks for the clarification, Ugis. Do you know why that is the case, of if it is stated anywhere? I did not see any note in the package vignette / manual regarding lack of support for RNA-Seq data. ...
written 15 months ago by Keith Hughitt100
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ArrayExpress unable to find raw data: "Experiment has no raw files available"
... Hello, I just tried using the ArrayExpress library for the first time to retrieve some RNA-Seq samples through the EBI ArrayExpress database. When I attempt to call the ArrayExpress function, however, I run into the following error: > library(ArrayExpress) ...
arrayexpress written 15 months ago by Keith Hughitt100 • updated 15 months ago by ugis10
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Comment: C: Why the package readr can't be find?
... Just to be clear, `ls ~/R/x86_64-pc-linux-gnu-library/3.3/readr/R/sysdata.rdb` shows the file exists in that location? What are the file permissions? ...
written 18 months ago by Keith Hughitt100

Latest awards to Keith Hughitt

Popular Question 12 months ago, created a question with more than 1,000 views. For Plotting an hclust sub-tree in WGCNA?
Popular Question 13 months ago, created a question with more than 1,000 views. For Plotting an hclust sub-tree in WGCNA?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For WGCNA: overlapping colors in plotDendroAndColors?
Supporter 2.7 years ago, voted at least 25 times.

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