Bioconductor Gff3

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dexseq python gtf gff3 annotation

5.0 years ago Raito92 ▴ 60

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annotation gff3 gff genome

updated 5.6 years ago by Michael Lawrence ★ 11k • written 5.6 years ago by mictadlo ▴ 10

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parclip bedtools bed files gff3

7.3 years ago linuxborg2 • 0

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txdb gff3 polycistronic transcript

7.5 years ago Piotr Gawronski • 0

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GenomicFeatures GFF3

updated 8.1 years ago by Valerie Obenchain ★ 6.8k • written 8.1 years ago by Dario Strbenac ★ 1.6k

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AnnotationHub Gencode GFF3 FASTA News

9.7 years ago Sonali Arora ▴ 390

6 results • Page 1 of 1

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Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0

There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…

Comment: Differing results with DESeq2 by JKim • 0

My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …

Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k

Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…

Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k

This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…

Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80

Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…

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remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline

How to remove X & Y chromosome genes from RNAseq data

Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?

A: Unbalanced experiment with multiple samples from each patient.

A: Understanding contrasts limma

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Autobiographer to Paul Harrison ▴ 100

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