Bioconductor Gff3

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dexseq python gtf gff3 annotation

5.8 years ago Raito92 ▴ 60

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annotation gff3 gff genome

updated 6.4 years ago by Michael Lawrence ★ 11k • written 6.5 years ago by mictadlo ▴ 10

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parclip bedtools bed files gff3

8.1 years ago linuxborg2 • 0

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txdb gff3 polycistronic transcript

8.3 years ago Piotr Gawronski • 0

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GenomicFeatures GFF3

updated 8.9 years ago by Valerie Obenchain ★ 6.8k • written 8.9 years ago by Dario Strbenac ★ 1.6k

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AnnotationHub Gencode GFF3 FASTA News

10.5 years ago Sonali Arora ▴ 390

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Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k

I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…

Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k

Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…

Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0

Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…

Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0

Hello, I was also wondering about the same issue. Did you figure it out?

Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0

FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…

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Answer: Which preprocessing steps are needed before running limpa?

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?

Answer: Which preprocessing steps are needed before running limpa?

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?

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Popular Question to Peter Hickey ▴ 760