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GAlignments
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reset
1
vote
3
replies
2.6k
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how to renameSeqlevels-GenomicAlignments
annotation
GAlignments
bamfileobject
renameseqlevels
7.3 years ago
teresati
▴ 10
2
votes
2
replies
1.3k
views
How to access metadata of GAlignments objects
rtracklayer
Rsamtools
GAlignments
GRanges
metadata
updated 4.0 years ago by
Hervé Pagès
16k • written 4.0 years ago by
Robert
▴ 10
2
votes
1
reply
1.1k
views
inconsistent results from applyPileups and pileLettersAt
Rsamtools
GAlignments
pileup
updated 8.0 years ago by
Martin Morgan
25k • written 8.0 years ago by
jesper.gadin
▴ 10
3
votes
1
reply
4.8k
views
Creating a count matrix from 8 bam files in R (RNAseq experiment)
deseq2
rnaseq
count matrix
galignments
granges
updated 6.9 years ago by
Michael Love
42k • written 6.9 years ago by
bananaal1
▴ 10
4 results • Page
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Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt
by
blackwidowzzz
• 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Votes
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
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