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genomeintervals
•
reset
2
votes
3
replies
675
views
GRanges object from gene list
granges
bed
genomicranges
genomeintervals
deseq2
4.4 years ago
rbronste
▴ 60
2
votes
1
reply
1.1k
views
Extracting UTRs from exon and CDS data
genomeintervals
UTRs
exons
CDS
GenomicRanges
updated 4.8 years ago by
Michael Lawrence
11k • written 4.8 years ago by
rubi
▴ 100
3
votes
2
replies
891
views
What is the main difference between nclist and intervaltree algorithm in GenomicRanges packages ?
nclist
genomeintervals
updated 6.3 years ago by
Hervé Pagès
15k • written 6.3 years ago by
Jurat Shahidin
▴ 70
0
votes
1
reply
849
views
cannot load genomeIntervals package
genomeIntervals
updated 6.9 years ago by
Nicolas Delhomme
▴ 320 • written 7.2 years ago by
mhz
• 0
1
vote
8
replies
1.1k
views
Bug: readGff3 isRightOpen should be FALSE
genomeintervals
updated 6.9 years ago by
Nicolas Delhomme
▴ 320 • written 6.9 years ago by
sjackman
• 0
0
votes
1
reply
2.1k
views
biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene") fails
BSgenome
hexbin
BSgenome
IRanges
genomeIntervals
GenomicRanges
girafe
Rsamtools
HiTC
HiTC
updated 9.2 years ago by
Dan Tenenbaum
★ 8.2k • written 9.2 years ago by
Wim Kreinen
▴ 100
0
votes
0
replies
632
views
convert "Genome_intervals_stranded" to "Genome_intervals"? (girafe)
Annotation
convert
genomeIntervals
Annotation
convert
genomeIntervals
10.3 years ago
delhomme@embl.de
★ 1.2k
0
votes
1
reply
650
views
gff files: how to tell if right-open interval convention used?
genomeIntervals
genomeIntervals
updated 11.2 years ago by
Hervé Pagès
15k • written 11.2 years ago by
Julien Gagneur
▴ 50
0
votes
0
replies
720
views
stranded findOverlaps
Sequencing
Annotation
GO
rtracklayer
IRanges
genomeIntervals
Sequencing
Annotation
GO
12.3 years ago
Robert Castelo
★ 2.9k
9 results • Page
1 of 1
Recent ...
Replies
Comment: Italicise
by
Pau
• 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa
by
priyanka.m
• 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
by
wahaha
• 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Comment: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
Thank you, @mikelove - that did it! The results make sense now. From my original post, could you clarify what the `group1w.sexfemale` contr…
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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