Admin: Neilfws

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Neilfws48k
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Sydney, Australia
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Data scientist and bioinformatician based in Sydney, Australia.

Posts by Neilfws

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Comment: C: How to match genes of one file to another but in multiple columns
... It's not clear to me from your question and example data how a gene ID from `archloro.txt` can match both IDs in one row of `ArabidopsisParalogue.txt`, when the IDs in the latter file are not identical. Could you clarify the question with some expected output? ...
written 3 months ago by Neilfws48k
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Answer: A: why sysID2product list for S. pombe is 2000 gene less than allnames list?
... I doubt that you are still eagerly awaiting an answer after more than 3 years :) but the answer seems to be that `sysID2product` contains only the known protein-coding genes ([as stated here][1]), whereas `allNames` as the name indicates contains all genes: protein-coding, non-coding RNA and pseudo ...
written 3 months ago by Neilfws48k
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Answer: A: Where can I find GPL571 cdf file?
... You can get CDF files [from this site][1]. You probably want the file beginning `hgu133a2hsentrezgcdf_19.0.0`. Alternatively it may be archived somewhere in the Affymetrix website. [1]: http://nmg-r.bioinformatics.nl/NuGO_R.html ...
written 4 months ago by Neilfws48k
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Answer: A: How can I calculate the number of sequences starting with different nucleotides
... As you mentioned that you normally work in R, I thought an R-based solution might be of interest. Good packages for working with sequences are Bioconductor's [Biostrings][1] and the older [seqinr][2]. Using `seqinr`, you can read in a fasta-formatted file like so: library(seqinr) myseqs & ...
written 4 months ago by Neilfws48k
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Answer: A: biomaRt mmusculus_gene_ensembl dataset
... The same is true of the Ensembl BioMart website and of other hosts *e.g.* `www.ensembl.org`. It appears that in the latest build 91, mouse data has been moved to "Mouse strains 91", or `ENSEMBL_MART_MOUSE`: listDatasets(useMart(host = "www.ensembl.org", biomart = "ENSEMBL_MART_MOUSE")) ...
written 6 months ago by Neilfws48k
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Answer: A: error bar in bar plot ggplot2
... You need to define what you mean by "error bars". You also need to think about what it is that you want to visualize and the most effective way to do that. I am assuming that for each gene, you want to calculate a summary statistic - the mean? - of the values for HSC3, CMP1 and Gran1, and that "err ...
written 6 months ago by Neilfws48k
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Comment: C: error bar in bar plot ggplot2
... I edited the title as your code specifies a bar plot, not a boxplot. ...
written 6 months ago by Neilfws48k
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Comment: C: How to avoid conversion of gene symbols to date format in Excel
... I believe (but am not 100% certain) that Google sheets did not suffer from the auto-conversion issue when this thread was started, but now it does. The "trick", as with Excel, is to define the column variable type of course. Unfortunately, getting people to think about the nature of their data in a ...
written 6 months ago by Neilfws48k
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Comment: C: Pca From Vcf Files
... [SNPRelate has been removed][1] from CRAN. You need to install it [from Bioconductor now][2]. [1]: https://cran.r-project.org/web/packages/SNPRelate/index.html [2]: https://bioconductor.org/packages/release/bioc/html/SNPRelate.html ...
written 7 months ago by Neilfws48k
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Comment: C: esearch in reutils package: how to specify dataset?
... Cross-posted to https://stackoverflow.com/questions/44532441/esearch-in-reutils-package-how-to-specify-dataset/44533151 where I answered. ...
written 12 months ago by Neilfws48k

Latest awards to Neilfws

Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How To Download Gene Sequences From Ncbi Gene
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How To Get Fasta Format Using Fastafrombed Or How To Turn Linearized Fasta To Th
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Scholar 4 months ago, created an answer that has been accepted. For A: Where Do I Find Genomic Coordinates For Human Cytogenetic Bands According To Ent
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