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Tutorial:
Gene Set Enrichment Analysis
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Tutorial:
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Tutorial:
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Comment: Ciriquant not configuring hisat2 indexed files
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Atul K.
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Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but …
Answer: GTF file from Stringtie to R Studio for either Ballgown or DESeq2
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Ram
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See this section on how to use tximport to import StringTie output for DESeq2 processing: https://bioconductor.org/packages/devel/bioc/vign…
Comment: how to find genes that are significantly expressed in brain cortex samples
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Ram
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Can you explain the normalization or give me a link that describes it, please? Comparison across samples will always be caveated as RNA-seq…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
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Ram
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Sorry, I see how harsh I come across. It's not good practice to use multiple versions of R in the same project. I can understand legacy pro…
Answer: MEGA Analysis Issue on High-Performance Computer
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Mensur Dlakic
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> I have ensured that I am using the latest version of MEGA and that other applications are not consuming excessive resources during the an…
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BioinfGuru
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Some of us are still learning and fall foul to knowledge limitation fairly regularly. Luckily we have people to put us in our place.
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> I know that I should be able to collect protein sequences from the blastp results into a file, but I do not know how to do this.
You c…
Comment: how to find genes that are significantly expressed in brain cortex samples
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rheab1230
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I got the normalized gene count from gtex portal. they use inverse quantile normalization
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Matthias Zepper
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It is not entirely off, but evidently also not correct.
Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
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Ram
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> so a single Rscript could utilise multiple environments and versions
How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples
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Ram
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Normalized how?
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With public data one has to work with what is there. If the information about position is absent then only thing that could be done is to l…
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BioinfGuru
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Or better yet. To have an R package that allows access to conda environments via "conda list env" so that environments can be switched with…
Comment: what's the genomic location and name of gene responsible for orange and black pa
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GenoMax
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If GPT is right then it says that:
> The specific gene responsible for the orange and non-orange (black or
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Jean-Karim Heriche
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As far as I know the Orange locus hasn't been mapped to a gene. Maybe this paper will help in narrowing the search: https://www.ncbi.nlm.ni…
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