Bioconductor GFF3

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dexseq python gtf gff3 annotation

5.5 years ago Raito92 ▴ 60

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annotation gff3 gff genome

updated 6.2 years ago by Michael Lawrence ★ 11k • written 6.2 years ago by mictadlo ▴ 10

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parclip bedtools bed files gff3

7.8 years ago linuxborg2 • 0

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txdb gff3 polycistronic transcript

8.0 years ago Piotr Gawronski • 0

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GenomicFeatures GFF3

updated 8.6 years ago by Valerie Obenchain ★ 6.8k • written 8.6 years ago by Dario Strbenac ★ 1.6k

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AnnotationHub Gencode GFF3 FASTA News

10.2 years ago Sonali Arora ▴ 390

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Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

Comment: deseq2 filter the low counts by empty_mt • 0

Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…

Comment: DESeq2 interactions by Michael Love 43k

GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …

Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k

We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you

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Answer: DESeq2 interactions

Answer: Important: Bioconductor Release 3.22 Delayed

A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

Answer: DESeq2 for candidate gene analysis

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