Showing : 2bit • reset
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News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 4.4 years ago by • 0 • written 4.4 years ago by 3.5k
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News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
4.6 years ago shepherl 3.5k
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News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
4.9 years ago shepherl 3.5k
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News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
5.2 years ago shepherl 3.5k
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News: ensembl 92 gtfs and fasta twobits have been added to AnnotationHub
ensembl gtf 2bit annotationhub News
5.4 years ago shepherl 3.5k
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News: ensembl 91 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit News
5.8 years ago shepherl 3.5k
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Error from BSgenome forge using .2bit file
BSgenome forge 2bit bsgnome forge 2bit file
updated 8.5 years ago by 16k • written 8.5 years ago by • 0
7 results • Page 1 of 1
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Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…
Votes
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
Answer: Batch correction and repeated measures
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