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Recent Replies
Comment: ChatGPT optimized for bioinformatics questions
by
Alexander
▴
100
May be you can consider to make a talk about that work for your community "sciBerloga" - see previous talks: https://www.youtube.com/@SciBe…
Answer: where to obtain hg19 reference transcriptome in gencode
by
GenoMax
130k
[**On this page**][1]
Transcriptome: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/GRCh37_mapping/gencode.v43lift…
Comment: GSEA application not launching
by
GenoMax
130k
If you have not, look in "System settings" and "security" to see if the OS is blocking the application from launching.
Comment: Decoding MM and ML tags in .SAM file
by
Alex Reynolds
35k
I made changes to how I decode m6A events and updated links in the answer above. Python code is in a separate repository. Javascript code i…
Comment: How do I calculate differential expression for RNA-seq values with the "limma" p
by
John
•
0
So the manual uses CPM instead of TPM. Do I need to adjust the formulae they use, or is it still the same?
Also, in the manual, it uses a …
Answer: synteny viewer
by
cmdcolin
★
3.0k
I compile a large list of visualization tools, here are all tools I have tagged "comparative" which can include synteny viewers https://cmd…
Comment: Limma returned only positive logFC values
by
melissachua90
▴
40
Thank you for your kind comments.
Comment: ChatGPT optimized for bioinformatics questions
by
Sasha
▴
360
hi Jesse - we're hoping to build custom lab specific private experiences for folks. You can check it out here and reach out if you're inter…
Comment: ChatGPT optimized for bioinformatics questions
by
Sasha
▴
360
This is awesome prodding. Will definitely try to address this use case; especially it being more explicit with the citations back to papers…
Answer: ChatGPT optimized for bioinformatics questions
by
Alexander
▴
100
Thanks for sharing !
I asked about score calculation answer is quite good , though the last example seems not fully correct
![enter i…
Comment: Filtering genes after TPM normalization
by
Meisam
▴
180
While not a fan of it, I’ve seen papers where authors used a cpm or tpm value cutoff of 1 to filter their count table. Since this threshold…
Answer: ChatGPT optimized for bioinformatics questions
by
Jesse
▴
600
It's very eager to provide code examples with Biopython, but the examples veer into the nonsensical at times:
![wait what][1]
It also…
Comment: Does adding reads cause batch effects?
by
bioinfo
▴
80
Would the number of reads in each batch affect the PCA? I do notice some batch effect. For example, I have one batch where most samples hav…
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