User: Anthony Nash

gravatar for Anthony Nash
Anthony Nash20
Reputation:
20
Status:
New User
Location:
University of Oxford
Last seen:
1 month, 3 weeks ago
Joined:
8 months, 1 week ago
Email:
d******************@googlemail.com

New to Bioconductor but not new to science!

A computational chemist (Molecular Dynamics and Quantum Chemistry) with a background in traditional and nature-inspired Artificial Intelligence, professionally trained software engineer, and now a clinical epidemiologist. Breaking into Cheminformatics as a bridge between everything! 

Posts by Anthony Nash

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Comment: C: Number and percent of mapped reads from RNA seq analysis.
... Isn't there a tool within Bioconductor suite that can do this rather than adding in further software? ...
written 8 weeks ago by Anthony Nash20
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Number and percent of mapped reads from RNA seq analysis.
... Sorry if this is a simple question for some, I am flying blind on my first attempt at RNA seq with a demand for immediate deadlines. I've used a process of Salmon (with FASTQC) -> tximport -> DESeq2 and I've thrown in a bit of Scater for some PCA calculations. however, I would like to plot th ...
rna rna-seq written 8 weeks ago by Anthony Nash20 • updated 8 weeks ago by Steve Lianoglou12k
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Bioactivity assay DBs for cheminfo packages
... I've started exploring the Cheminformatics capabilities of Bioconductor, notably through the combination of the packages: ChemmineR, fmcsR, bioassayR and biomaRt. I am very interested in exploiting any publicly available drug-target activity assay databases e.g., PubChem, which is supported by the b ...
chemminer bioassayr pubchem written 10 weeks ago by Anthony Nash20 • updated 10 weeks ago by Thomas Girke1.7k
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Answer: A: Where can I locate the bioassayR database?
... I contacted the site admins and they providing the following link that works: http://biocluster.ucr.edu/~tbackman/bioassayR/pubchem_protein_only.sqlite ...
written 11 weeks ago by Anthony Nash20
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Where can I locate the bioassayR database?
... I am reading the BioassayR guide on prebuilt PubChem Bioassay DBs: https://www.bioconductor.org/packages/release/bioc/vignettes/bioassayR/inst/doc/bioassayR.html#prebuilt-database-example-investigate-activity-of-a-known-drug And, the embedded link to the database http://chemmine.ucr.edu/bioassayr/ ...
cheminformatics chemminer bioassayr written 11 weeks ago by Anthony Nash20
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Comment: C: How to remove HCL mols in Chemminer
... That's great! I'll be using your excellent ChemmineR package quite a lot over the next 6 months. If I find anything else, I'll post it to Bioconductor support forums (in case it's a likely oversight on my behalf). ...
written 11 weeks ago by Anthony Nash20
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Comment: C: How to remove HCL mols in Chemminer
... Some CIDs with a mismatch of additional compounds e.g., dihydrochloride, bromide, etc. 6434889 1979 6420038 5281082 245005 5763 76971380 102678 123606 441325 11065 60496 2170 9301 60795 2247 54360 5362123 23705 8478 7699 2346 50088 12456 5702220 31100 2448 64737 2480 23724817 5831 90010 40127 2585 2 ...
written 12 weeks ago by Anthony Nash20
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Comment: C: How to remove HCL mols in Chemminer
... [In place of my earlier email] Hi Thomas, I would be happy to send across the code once I finished compiling my CID list. I'll post a small code snippet here. I am very new to cheminformatics; in your experience, would removing dihydro/hydro/chlorides, bromides etc., from an SDF entry within R be ...
written 12 weeks ago by Anthony Nash20
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How to remove HCL mols in Chemminer
... I am pulling down an SDFset of drugs from PubChem using the drug CIDs. There isn't an absolute match between our experimental drug list and those on PubChem. They differ by the include/exclusion of HCL molecules. For now, we would like to do maximum similarity matches between the root drug i.e., wit ...
chemminer chemistry written 12 weeks ago by Anthony Nash20 • updated 7 weeks ago by khoran0

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