Admin: Neilfws

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Neilfws48k
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Sydney, Australia
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6 months ago
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10 years, 5 months ago
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Data scientist and bioinformatician based in Sydney, Australia.

Posts by Neilfws

<prev • 2,763 results • page 1 of 277 • next >
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Answer: A: How to run several one-way ANOVAs in R using on different categories?
... One approach is to `nest` the data in a data frame with a list column. You can then use `purrr::map` to run a function for each group, `tidy` the results and `unnest`. Using the same `df1` as in the answer from @zx8754: library(dplyr) library(tidyr) library(purrr) df1 %>% ...
written 12 months ago by Neilfws48k
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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 2.4 years 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 2.4 years 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 2.5 years 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 2.5 years 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 2.6 years 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 2.6 years 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 2.6 years 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 2.7 years 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 2.7 years ago by Neilfws48k

Latest awards to Neilfws

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How To Annotate A Previously Unknown Bacterial Organism With Glimmer3?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Scholar 8 months ago, created an answer that has been accepted. For A: How do experienced people look for full reference genomes?
Scholar 8 months ago, created an answer that has been accepted. For A: Gene symbols to Entrez Gene ID for S. pombe
Scholar 8 months ago, created an answer that has been accepted. For A: Drawing Dssp File
Appreciated 8 months ago, created a post with more than 5 votes. For A: Generating Codon Usage
Great Question 9 months ago, created a question with more than 5,000 views. For Xml Returned Using Efetch Differs To That Downloaded From Query At Pubmed Website
Appreciated 10 months ago, created a post with more than 5 votes. For A: Mirna Target Prediction
Appreciated 10 months ago, created a post with more than 5 votes. For A: Is The Biostar Fading? (Updated For 2014)
Scholar 11 months ago, created an answer that has been accepted. For A: Drawing Dssp File
Teacher 11 months 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
Scholar 11 months ago, created an answer that has been accepted. For A: Is the source code for the NCBI-BLAST service available anywhere?
Epic Question 12 months ago, created a question with more than 10,000 views. For Your Thoughts On A "Standard" Pipeline To Process Illumina 450K Data
Teacher 12 months 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
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: What Is Parsimonious Fashion ?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Problem With Awk Printing
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: How To Annotate A Previously Unknown Bacterial Organism With Glimmer3?
Teacher 2.0 years 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
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Scholar 2.0 years ago, created an answer that has been accepted. For A: How do experienced people look for full reference genomes?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Search through thousands of fasta sequences via the description field of the hea
Scholar 2.0 years ago, created an answer that has been accepted. For A: Gene symbols to Entrez Gene ID for S. pombe
Scholar 2.0 years ago, created an answer that has been accepted. For A: Is the source code for the NCBI-BLAST service available anywhere?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Bioperl-Based Script To Parse Multiple Uniprot Records Hangs Unexpectedly
Good Answer 2.0 years ago, created an answer that was upvoted at least 5 times. For A: Collapse Probes For Same Gene

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