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gff3
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DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq
python
gtf
gff3
annotation
4.0 years ago
Raito92
▴ 60
2
votes
2
replies
1.9k
views
Filtering GFF3 file
annotation
gff3
gff
genome
updated 4.6 years ago by
Michael Lawrence
★ 11k • written 4.6 years ago by
mictadlo
▴ 10
0
votes
0
replies
972
views
I need to measure distance of PAR-CLIP data to RNA regions
parclip
bedtools
bed files
gff3
6.3 years ago
linuxborg2
• 0
2
votes
2
replies
4.4k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb
gff3
polycistronic transcript
6.5 years ago
Piotr Gawronski
• 0
9
votes
3
replies
3.0k
views
Importing Gene Symbols with makeTxDbFromGFF
GenomicFeatures
GFF3
updated 7.1 years ago by
Valerie Obenchain
★ 6.8k • written 7.1 years ago by
Dario Strbenac
★ 1.5k
2
votes
0
replies
3.3k
views
News:
Gencode GFF3 and FASTA files now available via AnnotationHub
AnnotationHub
Gencode
GFF3
FASTA
News
8.7 years ago
Sonali Arora
▴ 390
6 results • Page
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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