Bioconductor Gff3

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dexseq python gtf gff3 annotation

4.8 years ago • updated 4.7 years ago Raito92 ▴ 60

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annotation gff3 gff genome

updated 5.4 years ago by Michael Lawrence ★ 11k • written 5.4 years ago by mictadlo ▴ 10

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parclip bedtools bed files gff3

7.0 years ago linuxborg2 • 0

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txdb gff3 polycistronic transcript

7.2 years ago Piotr Gawronski • 0

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GenomicFeatures GFF3

updated 7.9 years ago by Valerie Obenchain ★ 6.8k • written 7.9 years ago by Dario Strbenac ★ 1.5k

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AnnotationHub Gencode GFF3 FASTA News

9.4 years ago Sonali Arora ▴ 390

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Comment: plyranges: find exact GRanges match keeping metadata columns by alexis.weinreb • 0

Thank you, this does clarify the available options.

Answer: displaying the differential expression with deseq2 over 4X2 samples with the in by James W. MacDonald 67k

If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated a…

Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by jodan • 0

Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…

Answer: Unused arguments error without used arguments in GSVA? by jodan • 0

It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and max…

Answer: Using genomicRanges / plyranges to calculate score of peaks within intervals by Michael Love 43k

This should be possible with plyranges using `join_overlap` and `group_by` on the metadata from the tile. E.g. create `tile.id` as a variab…

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Answer: Find exact GRanges match keeping metadata columns

Answer: Unused arguments error without used arguments in GSVA?

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