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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
5.0 years ago
Raito92
▴ 60
2
votes
2
replies
2.4k
views
Filtering GFF3 file
annotation
gff3
gff
genome
updated 5.6 years ago by
Michael Lawrence
★ 11k • written 5.6 years ago by
mictadlo
▴ 10
0
votes
0
replies
1.2k
views
I need to measure distance of PAR-CLIP data to RNA regions
parclip
bedtools
bed files
gff3
7.3 years ago
linuxborg2
• 0
2
votes
2
replies
5.2k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb
gff3
polycistronic transcript
7.5 years ago
Piotr Gawronski
• 0
9
votes
3
replies
3.7k
views
Importing Gene Symbols with makeTxDbFromGFF
GenomicFeatures
GFF3
updated 8.1 years ago by
Valerie Obenchain
★ 6.8k • written 8.1 years ago by
Dario Strbenac
★ 1.6k
2
votes
0
replies
4.0k
views
News:
Gencode GFF3 and FASTA files now available via AnnotationHub
AnnotationHub
Gencode
GFF3
FASTA
News
9.7 years ago
Sonali Arora
▴ 390
6 results • Page
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Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
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.
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