Bioconductor Refseq

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976

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refseq Bioconductor conversion

3.9 years ago heiko_kin ▴ 60

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653

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RefSeq Chromosome Mutalyzer

4.6 years ago heiko_kin ▴ 60

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2.3k

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tximport Gene IDs txdb RefSeq Salmon

updated 4.8 years ago by Michael Love 42k • written 4.8 years ago by holmkn • 0

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3.1k

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edgeR ENEMBL RefSeq

updated 5.6 years ago by Gordon Smyth 51k • written 5.6 years ago by mzillur • 0

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2.7k

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genomicfeatures maketxdbfromucsc refseq

updated 8.3 years ago by Hervé Pagès 16k • written 8.3 years ago by Sebastien Vigneau ▴ 10

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3.9k

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ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb

updated 8.8 years ago by Hervé Pagès 16k • written 8.8 years ago by gokcen.eraslan ▴ 10

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3.0k

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promoter granges refseq ucsc organismdb

updated 8.9 years ago by Robert Castelo ★ 3.4k • written 8.9 years ago by efoss ▴ 10

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3.9k

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refseq annotationhub

updated 9.1 years ago by Martin Morgan 25k • written 9.1 years ago by dalloliogm ▴ 50

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1.8k

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customprodb dbsnp refseq varianttools

updated 9.3 years ago by xiaojing.wang ▴ 50 • written 9.3 years ago by kristenbeck527 • 0

9 results • Page 1 of 1

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Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim by Gordon Smyth 51k

`nec` computes one set of negative control parameters (mu, sigma, alpha) for each sample.

Comment: DESeq Input from Salmon + tximport/tximeta by LuciaNhu • 0

Thank you to the author for the quick reply. If I use `gene_counts_length_scaled.tsv` as a metric that has already normalized for library s…

Answer: DESeq Input from Salmon + tximport/tximeta by Michael Love 42k

Given nf-core's pipeline here, you can use rounded counts from `gene_counts_length_scaled.tsv`.

Comment: Question about using LRT test for time course experiments with DESeq2 by James W. MacDonald 67k

You don't want to add a logFC on top like that, as it invalidates the p-value. Maybe I wasn't clear before. The LRT gives you all the gene…

Comment: Question about using LRT test for time course experiments with DESeq2 by Denise • 0

Hi James, Thank you very much for your very detailed explanation! I guess my question is simpler than that, I just want to union, across…

Votes

Answer: DESeq Input from Salmon + tximport/tximeta

Answer: featureCounts segmentation fault with large chromosomes

Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion

Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu

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