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genomeintervals
•
reset
0
votes
0
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108
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
4 weeks ago
gshweta95
• 0
2
votes
3
replies
1.4k
views
GRanges object from gene list
granges
bed
genomicranges
genomeintervals
deseq2
6.3 years ago
rbronste
▴ 60
2
votes
1
reply
1.6k
views
Extracting UTRs from exon and CDS data
genomeintervals
UTRs
exons
CDS
GenomicRanges
updated 6.7 years ago by
Michael Lawrence
★ 11k • written 6.7 years ago by
rubi
▴ 110
3
votes
2
replies
1.3k
views
What is the main difference between nclist and intervaltree algorithm in GenomicRanges packages ?
nclist
genomeintervals
updated 8.2 years ago by
Hervé Pagès
16k • written 8.2 years ago by
Jurat Shahidin
▴ 80
0
votes
1
reply
1.2k
views
cannot load genomeIntervals package
genomeIntervals
updated 8.8 years ago by
Nicolas Delhomme
▴ 320 • written 9.1 years ago by
mhz
• 0
1
vote
8
replies
1.6k
views
Bug: readGff3 isRightOpen should be FALSE
genomeintervals
updated 8.8 years ago by
Nicolas Delhomme
▴ 320 • written 8.9 years ago by
sjackman
• 0
0
votes
1
reply
2.6k
views
biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene") fails
BSgenome
hexbin
BSgenome
IRanges
genomeIntervals
GenomicRanges
girafe
Rsamtools
HiTC
HiTC
updated 11.1 years ago by
Dan Tenenbaum
★ 8.2k • written 11.1 years ago by
Wim Kreinen
▴ 100
0
votes
0
replies
879
views
convert "Genome_intervals_stranded" to "Genome_intervals"? (girafe)
Annotation
convert
genomeIntervals
Annotation
convert
genomeIntervals
12.2 years ago
delhomme@embl.de
★ 1.2k
0
votes
1
reply
915
views
gff files: how to tell if right-open interval convention used?
genomeIntervals
genomeIntervals
updated 13.1 years ago by
Hervé Pagès
16k • written 13.1 years ago by
Julien Gagneur
▴ 50
0
votes
0
replies
1.0k
views
stranded findOverlaps
Sequencing
Annotation
GO
rtracklayer
IRanges
genomeIntervals
Sequencing
Annotation
GO
14.2 years ago
Robert Castelo
★ 3.3k
10 results • Page
1 of 1
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Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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