Admin: Neilfws

gravatar for Neilfws
Neilfws48k
Reputation:
48,090
Status:
Trusted
Location:
Sydney, Australia
Website:
http://nsaunders.wordp...
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 4 days ago
Joined:
9 years, 7 months ago
Email:
n******@gmail.com

Data scientist and bioinformatician based in Sydney, Australia.

Posts by Neilfws

<prev • 2,766 results • page 1 of 277 • next >
4
votes
3
answers
383
views
3
answers
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 3 months ago by Neilfws48k
2
votes
6
answers
1.5k
views
6
answers
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 19 months ago by Neilfws48k
1
vote
1
answer
1.1k
views
1
answers
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 19 months ago by Neilfws48k
1
vote
1
answer
564
views
1
answers
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 20 months ago by Neilfws48k
3
votes
2
answers
967
views
2
answers
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 20 months ago by Neilfws48k
1
vote
3
answers
4.6k
views
3
answers
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 22 months ago by Neilfws48k
3
votes
3
answers
2.1k
views
3
answers
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 22 months ago by Neilfws48k
0
votes
3
answers
2.1k
views
3
answers
Comment: C: error bar in bar plot ggplot2
... I edited the title as your code specifies a bar plot, not a boxplot. ...
written 22 months ago by Neilfws48k
1
vote
5
answers
4.6k
views
5
answers
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 23 months ago by Neilfws48k
0
votes
3
answers
20k
views
3
answers
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 23 months ago by Neilfws48k

Latest awards to Neilfws

Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Is The Biostar Fading? (Updated For 2014)
Scholar 7 weeks ago, created an answer that has been accepted. For A: Drawing Dssp File
Teacher 8 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
Scholar 8 weeks ago, created an answer that has been accepted. For A: Is the source code for the NCBI-BLAST service available anywhere?
Epic Question 11 weeks ago, created a question with more than 10,000 views. For Your Thoughts On A "Standard" Pipeline To Process Illumina 450K Data
Teacher 11 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
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: What Is Parsimonious Fashion ?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Problem With Awk Printing
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How To Annotate A Previously Unknown Bacterial Organism With Glimmer3?
Teacher 15 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
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Limit Upvotes Over A Certain Amount Of Hours
Scholar 15 months ago, created an answer that has been accepted. For A: How do experienced people look for full reference genomes?
Scholar 15 months ago, created an answer that has been accepted. For A: Search through thousands of fasta sequences via the description field of the hea
Scholar 15 months ago, created an answer that has been accepted. For A: Gene symbols to Entrez Gene ID for S. pombe
Scholar 15 months ago, created an answer that has been accepted. For A: Is the source code for the NCBI-BLAST service available anywhere?
Popular Question 15 months ago, created a question with more than 1,000 views. For Bioperl-Based Script To Parse Multiple Uniprot Records Hangs Unexpectedly
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Collapse Probes For Same Gene
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Perl Script To Make Statistics Of Mirna Abundances For Many Samples
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Does Anyone Know Of A Comprehensive List Of Bioinformatics Tools That Is Kept Ve
Appreciated 15 months ago, created a post with more than 5 votes. For A: Downloading And Maintaining A Local, Blast-Able Nr Database
Appreciated 15 months ago, created a post with more than 5 votes. For A: Can'T Locate Vcf.Pm Vcftools
Appreciated 15 months ago, created a post with more than 5 votes. For A: Library / Module For Network Analysis
Appreciated 15 months ago, created a post with more than 5 votes. For A: Collapse Probes For Same Gene
Appreciated 15 months ago, created a post with more than 5 votes. For A: Perl Script To Make Statistics Of Mirna Abundances For Many Samples

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 3191 users visited in the last hour