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Showing :
Coverage
•
reset
6
votes
3
replies
3.1k
views
how does coverage() works
biostrings
coverage
rle
iranges
8.7 years ago
likeeatingpizza
▴ 10
6
votes
0
replies
3.3k
views
BH vs BY in p.adjust + FDR interpretation
Coverage
limma
18.6 years ago • updated 9.1 years ago
Gordon Smyth
52k
5
votes
2
replies
3.4k
views
Gviz - show plus and minus strand from a bam
Sequencing
Coverage
Gviz
Sequencing
Coverage
Gviz
updated 11.3 years ago by
florian.hahne@novartis.com
★ 1.6k • written 11.3 years ago by
António Miguel de Jesus Domingues
▴ 510
5
votes
3
replies
2.0k
views
Calling coverage on GRanges object yields small negative values
granges
coverage
updated 9.9 years ago by
Hervé Pagès
16k • written 9.9 years ago by
Anya
▴ 10
4
votes
2
replies
1.9k
views
bamsignals - bamcoverage has no strand-specific option??
BAM
bamsignals
Coverage
updated 8.1 years ago by
helmuth
• 0 • written 8.1 years ago by
gtho123
▴ 40
3
votes
2
replies
2.2k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug
genomicranges
granges
rlelist
coverage
updated 7.0 years ago by
Hervé Pagès
16k • written 7.0 years ago by
xiaotong.yao23
▴ 10
3
votes
4
replies
1.4k
views
Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage
DESeq2
3.4 years ago
Rui
▴ 10
2
votes
6
replies
3.1k
views
Shrink or Expand RLE
RLE
iranges
granges
coverage
updated 9.9 years ago by
Martin Morgan
25k • written 9.9 years ago by
gen
▴ 30
2
votes
3
replies
1.8k
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage
s4vectors
seqlengths
9.0 years ago
liz.ingsimmons
▴ 140
2
votes
5
replies
2.3k
views
GOseq: count bias correction variations?
Coverage
goseq
updated 7.8 years ago by
Gordon Smyth
52k • written 10.6 years ago by
Christopher Conley
▴ 40
2
votes
6
replies
1.6k
views
Using edgeR with "traditional" coverage data?
edger
rnaseq
coverage
updated 8.8 years ago by
Ryan C. Thompson
★ 7.9k • written 8.8 years ago by
bastien.chevreux
• 0
1
vote
3
replies
4.3k
views
Blast analysis of two sequences in R
Coverage
Coverage
updated 10.8 years ago by
Martin Morgan
25k • written 10.8 years ago by
prabhakar ghorpade
▴ 100
1
vote
2
replies
1.8k
views
Gviz off-by-one with STAR BAM
gviz
off-by-one
STAR
BAM
coverage
updated 7.9 years ago by
Martin Morgan
25k • written 7.9 years ago by
bernt.popp
• 0
1
vote
2
replies
3.0k
views
"Normalising" GRanges coverage object
Coverage
GO
Gviz
Coverage
GO
Gviz
updated 10.5 years ago by
Ryan C. Thompson
★ 7.9k • written 10.5 years ago by
Aliaksei Holik
▴ 350
1
vote
0
replies
2.0k
views
pileup coverage from BAM file
Coverage
Cancer
IRanges
GenomicRanges
Coverage
Cancer
IRanges
GenomicRanges
12.0 years ago
Martin Morgan
25k
1
vote
3
replies
2.5k
views
views on Rle using GRanges object
RNASeq
Coverage
GO
Cancer
bridge
rtracklayer
IRanges
RNASeq
Coverage
GO
Cancer
bridge
updated 10.9 years ago by
Hervé Pagès
16k • written 10.9 years ago by
Michael Lawrence
★ 11k
1
vote
2
replies
2.2k
views
Does coverage() split exon spanning RNA-seq reads?
coverage
genomicranges
genomicalignments
updated 9.6 years ago by
Martin Morgan
25k • written 9.6 years ago by
Jake
▴ 90
1
vote
2
replies
1.8k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments
splicing
coverage
updated 5.4 years ago by
Michael Lawrence
★ 11k • written 7.9 years ago by
rasi1983
▴ 10
0
votes
0
replies
840
views
X:Map and 1.0 ST Gene Arrays, Introns
Coverage
probe
Coverage
probe
16.6 years ago
Thomas Hampton
▴ 750
0
votes
3
replies
1.4k
views
gene2pathway retrain: which model is more complete?
Genetics
Coverage
biomaRt
gene2pathway
Genetics
Coverage
biomaRt
gene2pathway
14.5 years ago
Bogdan
▴ 50
0
votes
1
reply
1.0k
views
tiling/SNP microarrays
SNP
Coverage
tilingArray
SNP
Coverage
tilingArray
updated 18.6 years ago by
Sean Davis
21k • written 18.6 years ago by
Jeffrey Blanchard
▴ 10
0
votes
4
replies
1.3k
views
Opinions on array design, normalization, and linear modeling with LIMMA
Sequencing
Coverage
Normalization
limma
Sequencing
Coverage
Normalization
limma
updated 17.3 years ago by
Yong Yin
▴ 60 • written 17.3 years ago by
Jianping Jin
▴ 890
0
votes
1
reply
981
views
IRanges:::coverage() speedup/enchancement
Coverage
IRanges
Coverage
IRanges
updated 15.2 years ago by
Michael Lawrence
▴ 620 • written 15.2 years ago by
Charles Berry
▴ 290
0
votes
5
replies
2.1k
views
read coverage per transcript for RNASeq
RNASeq
Coverage
PROcess
ShortRead
RNASeq
Coverage
PROcess
ShortRead
updated 15.5 years ago by
Martin Morgan
25k • written 15.5 years ago by
Jessica Hunter
▴ 40
0
votes
2
replies
1.2k
views
IRanges:::coverage() speedup/enchancement
Coverage
IRanges
Coverage
IRanges
updated 15.2 years ago by
Charles Berry
▴ 290 • written 15.2 years ago by
Patrick Aboyoun
★ 1.6k
0
votes
1
reply
969
views
"islands" and number of reads in the island in package chipseq/ShortRead
ChIPSeq
Coverage
chipseq
ChIPSeq
Coverage
chipseq
updated 15.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 15.2 years ago by
Nora Rieber
▴ 40
0
votes
1
reply
3.4k
views
color key - heatmap.2
Coverage
Coverage
updated 15.0 years ago by
Sean Davis
21k • written 15.0 years ago by
Amit Indap
▴ 10
0
votes
0
replies
1.0k
views
request: calculate coverage with weight on RangedData object
Coverage
Cancer
IRanges
Coverage
Cancer
IRanges
14.9 years ago
Janet Young
▴ 740
0
votes
1
reply
1.4k
views
loop over IRanges spaces
Coverage
convert
rtracklayer
ASSIGN
Coverage
convert
rtracklayer
ASSIGN
updated 14.8 years ago by
Michael Lawrence
★ 11k • written 14.8 years ago by
Yvan
▴ 60
0
votes
2
replies
1.1k
views
next-generation sequencing and embryogenisis
Sequencing
SAGE
Coverage
Sequencing
SAGE
Coverage
updated 14.6 years ago by
Steve Shen
▴ 330 • written 14.6 years ago by
Ziping Zhang
▴ 20
0
votes
3
replies
3.7k
views
from RefSeq to GO terms / gene symbol to geneID
Proteomics
Coverage
Annotation
GO
Proteomics
Coverage
Annotation
GO
17.7 years ago
Simon Lin
▴ 270
0
votes
0
replies
1.7k
views
New Quantian releases with almost all of CRAN / BioC
Coverage
Visualization
GUI
Coverage
Visualization
GUI
19.0 years ago
Dirk Eddelbuettel
▴ 80
0
votes
1
reply
1.6k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage
Annotation
GO
Cancer
Organism
edgeR
DESeq
GenomicRanges
Rsubread
easyRNASeq
GO
updated 11.2 years ago by
Nicolas Delhomme
▴ 320 • written 11.2 years ago by
Gordon Smyth
52k
0
votes
0
replies
5.5k
views
Reading GFF files into R and GenomeGraphs
Coverage
Annotation
Visualization
convert
GLAD
GenomeGraphs
rtracklayer
IRanges
Coverage
15.5 years ago
Michael Dondrup
▴ 140
0
votes
2
replies
1.4k
views
interoperability between IRanges/ShortRead and rtracklayer
Coverage
rtracklayer
IRanges
Coverage
rtracklayer
IRanges
updated 15.7 years ago by
Patrick Aboyoun
★ 1.6k • written 15.7 years ago by
Simon Anders
▴ 150
0
votes
0
replies
970
views
from RefSeq GI protein identifiers to GO terms
Proteomics
Coverage
GO
Proteomics
Coverage
GO
17.7 years ago
Lina Hultin-Rosenberg
▴ 80
0
votes
0
replies
1.1k
views
Ensembl mart release 54: Useful information
Coverage
zebrafish
Coverage
zebrafish
15.8 years ago
Rhoda Kinsella
▴ 660
0
votes
2
replies
1.2k
views
raw counts for edgeR
Coverage
Coverage
updated 13.8 years ago by
Sean Davis
21k • written 13.8 years ago by
Lana Schaffer
★ 1.3k
0
votes
0
replies
1.1k
views
rtracklayer
Coverage
Cancer
Coverage
Cancer
13.8 years ago
Michael Lawrence
★ 11k
0
votes
1
reply
1.5k
views
A CGH platform question
SNP
Genetics
Coverage
CGH
affy
SNP
Genetics
Coverage
CGH
affy
updated 16.2 years ago by
Henrik Bengtsson
★ 2.4k • written 16.2 years ago by
Johan Lindberg
▴ 70
0
votes
3
replies
2.8k
views
Any package to calculate NGS coverage and plot it?
Coverage
Coverage
13.7 years ago
Xiaohui Wu
▴ 280
0
votes
4
replies
1.5k
views
IRanges: Request for a "step" argument in runsum
Coverage
Annotation
Cancer
PROcess
IRanges
genomes
Coverage
Annotation
Cancer
PROcess
updated 13.6 years ago by
Hervé Pagès
16k • written 13.7 years ago by
Arnaud Amzallag
▴ 100
0
votes
8
replies
3.6k
views
views on Rle using GRanges object
RNASeq
Coverage
GO
rtracklayer
RNASeq
Coverage
GO
rtracklayer
updated 13.5 years ago by
Hervé Pagès
16k • written 13.5 years ago by
Janet Young
▴ 740
0
votes
1
reply
1.1k
views
strand consistency with readAligned, coverage and transcriptsBy
Coverage
Coverage
updated 13.4 years ago by
Steve Lianoglou
★ 13k • written 13.4 years ago by
Tefina Paloma
▴ 220
0
votes
17
replies
2.5k
views
Coverage by base
Coverage
Coverage
13.4 years ago
rohan bareja
▴ 200
0
votes
2
replies
989
views
Coverage of reads in 3'UTR
Coverage
Coverage
13.4 years ago • updated 13.3 years ago
rohan bareja
▴ 200
0
votes
0
replies
1.1k
views
Using DESeq with ChIP-seq data - all or non-redundant reads?
Coverage
Kidney
DESeq
Coverage
Kidney
DESeq
13.3 years ago
Ivan Gregoretti
▴ 310
0
votes
0
replies
1.0k
views
Normalization in Coverage
Coverage
Normalization
Coverage
Normalization
13.3 years ago
rohan bareja
▴ 200
0
votes
3
replies
1.6k
views
Normalization in Coverage
Coverage
Normalization
Coverage
Normalization
13.3 years ago
rohan bareja
▴ 200
0
votes
0
replies
1.6k
views
easyRNASeq: Number of total counts
GeneExpression
RNASeq
Genetics
Coverage
Normalization
BSgenome
Biobase
Biostrings
biomaRt
10.9 years ago
Guest User
★ 13k
50 results • Page
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Comment: How to formulate 2 factor nested design in DESeq2
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• 0
Hi JK Kim, I'm having a problem similar to the one you reported. Could you please tell me how you solved this problem? Thanks
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Thank you
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by
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Without providing a self-contained example, nobody can tell you if/where you went wrong. Since you get a KEGG pathway with some of the gene…
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We don't have a test of differential variance but other Bioconductor packages can, check similar posts (even on the right side bar) or use …
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