User: Keith Hughitt

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Keith Hughitt120
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Posts by Keith Hughitt

<prev • 55 results • page 1 of 6 • next >
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Best practices for sharing RMarkdown-based supplemental PDFs?
... Greetings! As I'm going through and cleaning up some RMarkdown-based analyses in preparation for inclusion as supplemental PDF's, I thought it might be interesting to see what kinds of things people consider "best practices" for generating these documents in such a way to make them maximally useful ...
knitr rmarkdown written 9 months ago by Keith Hughitt120 • updated 9 months ago by Aaron Lun25k
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Comment: C: rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
... Good call. I ran into the same issue, and after trying `base::rowSums()` with no success, was left clueless. I wonder if perhaps Bioconductor should be updated so-as to better detect sparse matrices and call the appropriate function? The current error message is not very informative. ...
written 16 months ago by Keith Hughitt120
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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 23 months ago by Keith Hughitt120
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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 2.4 years ago by Keith Hughitt120
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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 2.4 years ago by Keith Hughitt120
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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 2.6 years ago by Keith Hughitt120
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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 2.6 years ago by Keith Hughitt120
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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 2.6 years ago by Keith Hughitt120 • updated 2.6 years ago by Martin Morgan ♦♦ 24k
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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 2.8 years ago by Keith Hughitt120
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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 3.0 years ago by Keith Hughitt120

Latest awards to Keith Hughitt

Popular Question 14 months ago, created a question with more than 1,000 views. For Plotting an hclust sub-tree in WGCNA?
Voter 2.4 years ago, voted more than 100 times.
Student 2.4 years ago, asked a question with at least 3 up-votes. For WGCNA: overlapping colors in plotDendroAndColors?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Plotting an hclust sub-tree in WGCNA?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Plotting an hclust sub-tree in WGCNA?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For WGCNA: overlapping colors in plotDendroAndColors?
Supporter 4.4 years ago, voted at least 25 times.

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