Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
coverage
•
reset
6
votes
3
replies
2.3k
views
how does coverage() works
biostrings
coverage
rle
iranges
7.8 years ago
likeeatingpizza
▴ 10
6
votes
0
replies
2.7k
views
BH vs BY in p.adjust + FDR interpretation
Coverage
limma
17.7 years ago • updated 8.2 years ago
Gordon Smyth
50k
5
votes
2
replies
3.1k
views
Gviz - show plus and minus strand from a bam
Sequencing
Coverage
Gviz
Sequencing
Coverage
Gviz
updated 10.4 years ago by
florian.hahne@novartis.com
★ 1.6k • written 10.4 years ago by
António Miguel de Jesus Domingues
▴ 490
5
votes
3
replies
1.7k
views
Calling coverage on GRanges object yields small negative values
granges
coverage
updated 9.0 years ago by
Hervé Pagès
16k • written 9.0 years ago by
Anya
▴ 10
4
votes
2
replies
1.5k
views
bamsignals - bamcoverage has no strand-specific option??
BAM
bamsignals
Coverage
updated 7.2 years ago by
helmuth
• 0 • written 7.2 years ago by
gtho123
▴ 40
3
votes
2
replies
1.8k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug
genomicranges
granges
rlelist
coverage
updated 6.1 years ago by
Hervé Pagès
16k • written 6.1 years ago by
xiaotong.yao23
▴ 10
3
votes
4
replies
987
views
Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage
DESeq2
2.5 years ago
Rui
▴ 10
2
votes
6
replies
2.7k
views
Shrink or Expand RLE
RLE
iranges
granges
coverage
updated 9.0 years ago by
Martin Morgan
25k • written 9.0 years ago by
gen
▴ 30
2
votes
3
replies
1.5k
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage
s4vectors
seqlengths
8.1 years ago
liz.ingsimmons
▴ 140
2
votes
5
replies
1.9k
views
GOseq: count bias correction variations?
Coverage
goseq
updated 7.0 years ago by
Gordon Smyth
50k • written 9.7 years ago by
Christopher Conley
▴ 40
2
votes
6
replies
1.3k
views
Using edgeR with "traditional" coverage data?
edger
rnaseq
coverage
updated 7.9 years ago by
Ryan C. Thompson
★ 7.9k • written 7.9 years ago by
bastien.chevreux
• 0
1
vote
3
replies
3.9k
views
Blast analysis of two sequences in R
Coverage
Coverage
updated 9.9 years ago by
Martin Morgan
25k • written 9.9 years ago by
prabhakar ghorpade
▴ 100
1
vote
2
replies
1.5k
views
Gviz off-by-one with STAR BAM
gviz
off-by-one
STAR
BAM
coverage
updated 7.0 years ago by
Martin Morgan
25k • written 7.0 years ago by
bernt.popp
• 0
1
vote
2
replies
2.6k
views
"Normalising" GRanges coverage object
Coverage
GO
Gviz
Coverage
GO
Gviz
updated 9.6 years ago by
Ryan C. Thompson
★ 7.9k • written 9.6 years ago by
Aliaksei Holik
▴ 350
1
vote
0
replies
1.9k
views
pileup coverage from BAM file
Coverage
Cancer
IRanges
GenomicRanges
Coverage
Cancer
IRanges
GenomicRanges
11.1 years ago
Martin Morgan
25k
1
vote
3
replies
2.1k
views
views on Rle using GRanges object
RNASeq
Coverage
GO
Cancer
bridge
rtracklayer
IRanges
RNASeq
Coverage
GO
Cancer
bridge
updated 10.0 years ago by
Hervé Pagès
16k • written 10.0 years ago by
Michael Lawrence
★ 11k
1
vote
2
replies
1.9k
views
Does coverage() split exon spanning RNA-seq reads?
coverage
genomicranges
genomicalignments
updated 8.7 years ago by
Martin Morgan
25k • written 8.7 years ago by
Jake
▴ 90
1
vote
2
replies
1.5k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments
splicing
coverage
updated 4.5 years ago by
Michael Lawrence
★ 11k • written 7.0 years ago by
rasi1983
▴ 10
0
votes
0
replies
703
views
X:Map and 1.0 ST Gene Arrays, Introns
Coverage
probe
Coverage
probe
15.7 years ago
Thomas Hampton
▴ 750
0
votes
3
replies
1.2k
views
gene2pathway retrain: which model is more complete?
Genetics
Coverage
biomaRt
gene2pathway
Genetics
Coverage
biomaRt
gene2pathway
13.6 years ago
Bogdan
▴ 50
0
votes
1
reply
871
views
tiling/SNP microarrays
SNP
Coverage
tilingArray
SNP
Coverage
tilingArray
updated 17.7 years ago by
Sean Davis
21k • written 17.7 years ago by
Jeffrey Blanchard
▴ 10
0
votes
4
replies
1.1k
views
Opinions on array design, normalization, and linear modeling with LIMMA
Sequencing
Coverage
Normalization
limma
Sequencing
Coverage
Normalization
limma
updated 16.4 years ago by
Yong Yin
▴ 60 • written 16.4 years ago by
Jianping Jin
▴ 890
0
votes
1
reply
824
views
IRanges:::coverage() speedup/enchancement
Coverage
IRanges
Coverage
IRanges
updated 14.3 years ago by
Michael Lawrence
▴ 620 • written 14.3 years ago by
Charles Berry
▴ 290
0
votes
5
replies
1.9k
views
read coverage per transcript for RNASeq
RNASeq
Coverage
PROcess
ShortRead
RNASeq
Coverage
PROcess
ShortRead
updated 14.6 years ago by
Martin Morgan
25k • written 14.6 years ago by
Jessica Hunter
▴ 40
0
votes
2
replies
1.1k
views
IRanges:::coverage() speedup/enchancement
Coverage
IRanges
Coverage
IRanges
updated 14.3 years ago by
Charles Berry
▴ 290 • written 14.3 years ago by
Patrick Aboyoun
★ 1.6k
0
votes
1
reply
817
views
"islands" and number of reads in the island in package chipseq/ShortRead
ChIPSeq
Coverage
chipseq
ChIPSeq
Coverage
chipseq
updated 14.3 years ago by
Kasper Daniel Hansen
★ 6.5k • written 14.3 years ago by
Nora Rieber
▴ 40
0
votes
1
reply
3.1k
views
color key - heatmap.2
Coverage
Coverage
updated 14.1 years ago by
Sean Davis
21k • written 14.1 years ago by
Amit Indap
▴ 10
0
votes
0
replies
895
views
request: calculate coverage with weight on RangedData object
Coverage
Cancer
IRanges
Coverage
Cancer
IRanges
14.0 years ago
Janet Young
▴ 740
0
votes
1
reply
1.2k
views
loop over IRanges spaces
Coverage
convert
rtracklayer
ASSIGN
Coverage
convert
rtracklayer
ASSIGN
updated 13.9 years ago by
Michael Lawrence
★ 11k • written 13.9 years ago by
Yvan
▴ 60
0
votes
2
replies
892
views
next-generation sequencing and embryogenisis
Sequencing
SAGE
Coverage
Sequencing
SAGE
Coverage
updated 13.7 years ago by
Steve Shen
▴ 330 • written 13.7 years ago by
Ziping Zhang
▴ 20
0
votes
3
replies
3.2k
views
from RefSeq to GO terms / gene symbol to geneID
Proteomics
Coverage
Annotation
GO
Proteomics
Coverage
Annotation
GO
16.8 years ago
Simon Lin
▴ 270
0
votes
0
replies
1.5k
views
New Quantian releases with almost all of CRAN / BioC
Coverage
Visualization
GUI
Coverage
Visualization
GUI
18.1 years ago
Dirk Eddelbuettel
▴ 80
0
votes
1
reply
1.3k
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 10.3 years ago by
Nicolas Delhomme
▴ 320 • written 10.3 years ago by
Gordon Smyth
50k
0
votes
0
replies
5.0k
views
Reading GFF files into R and GenomeGraphs
Coverage
Annotation
Visualization
convert
GLAD
GenomeGraphs
rtracklayer
IRanges
Coverage
14.6 years ago
Michael Dondrup
▴ 140
0
votes
2
replies
1.2k
views
interoperability between IRanges/ShortRead and rtracklayer
Coverage
rtracklayer
IRanges
Coverage
rtracklayer
IRanges
updated 14.8 years ago by
Patrick Aboyoun
★ 1.6k • written 14.8 years ago by
Simon Anders
▴ 150
0
votes
0
replies
850
views
from RefSeq GI protein identifiers to GO terms
Proteomics
Coverage
GO
Proteomics
Coverage
GO
16.8 years ago
Lina Hultin-Rosenberg
▴ 80
0
votes
0
replies
913
views
Ensembl mart release 54: Useful information
Coverage
zebrafish
Coverage
zebrafish
14.9 years ago
Rhoda Kinsella
▴ 660
0
votes
2
replies
1.1k
views
raw counts for edgeR
Coverage
Coverage
updated 12.9 years ago by
Sean Davis
21k • written 12.9 years ago by
Lana Schaffer
★ 1.3k
0
votes
0
replies
942
views
rtracklayer
Coverage
Cancer
Coverage
Cancer
12.9 years ago
Michael Lawrence
★ 11k
0
votes
1
reply
1.3k
views
A CGH platform question
SNP
Genetics
Coverage
CGH
affy
SNP
Genetics
Coverage
CGH
affy
updated 15.3 years ago by
Henrik Bengtsson
★ 2.4k • written 15.3 years ago by
Johan Lindberg
▴ 70
0
votes
3
replies
2.5k
views
Any package to calculate NGS coverage and plot it?
Coverage
Coverage
12.8 years ago
Xiaohui Wu
▴ 280
0
votes
4
replies
1.2k
views
IRanges: Request for a "step" argument in runsum
Coverage
Annotation
Cancer
PROcess
IRanges
genomes
Coverage
Annotation
Cancer
PROcess
updated 12.7 years ago by
Hervé Pagès
16k • written 12.8 years ago by
Arnaud Amzallag
▴ 100
0
votes
8
replies
3.3k
views
views on Rle using GRanges object
RNASeq
Coverage
GO
rtracklayer
RNASeq
Coverage
GO
rtracklayer
updated 12.6 years ago by
Hervé Pagès
16k • written 12.6 years ago by
Janet Young
▴ 740
0
votes
1
reply
880
views
strand consistency with readAligned, coverage and transcriptsBy
Coverage
Coverage
updated 12.5 years ago by
Steve Lianoglou
★ 13k • written 12.6 years ago by
Tefina Paloma
▴ 220
0
votes
17
replies
2.1k
views
Coverage by base
Coverage
Coverage
12.5 years ago
rohan bareja
▴ 200
0
votes
2
replies
844
views
Coverage of reads in 3'UTR
Coverage
Coverage
12.5 years ago • updated 12.4 years ago
rohan bareja
▴ 200
0
votes
0
replies
944
views
Using DESeq with ChIP-seq data - all or non-redundant reads?
Coverage
Kidney
DESeq
Coverage
Kidney
DESeq
12.4 years ago
Ivan Gregoretti
▴ 310
0
votes
0
replies
917
views
Normalization in Coverage
Coverage
Normalization
Coverage
Normalization
12.4 years ago
rohan bareja
▴ 200
0
votes
3
replies
1.4k
views
Normalization in Coverage
Coverage
Normalization
Coverage
Normalization
12.4 years ago
rohan bareja
▴ 200
0
votes
0
replies
1.4k
views
easyRNASeq: Number of total counts
GeneExpression
RNASeq
Genetics
Coverage
Normalization
BSgenome
Biobase
Biostrings
biomaRt
10.0 years ago
Guest User
★ 13k
50 results • Page
1 of 1
Recent ...
Replies
Comment: fgsea fork
by
Sofa
• 0
Workshops and summer schools offer immersive learning experiences outside traditional academic settings, catering to diverse interests and …
Comment: limma models out of memory issue on Slurm HPC
by
SamGG
▴ 330
> Alternatively you could run each linear model fit (var1 to var6) in a separate batch run, and again that would presumably work. I think …
Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Awards
• All
Popular Question
to
Dario Strbenac
★ 1.5k
Popular Question
to
Ankit
▴ 20
Popular Question
to
michael.s
• 0
Popular Question
to
James W. MacDonald
65k
Popular Question
to
Pierre Lindenbaum
▴ 10
Locations
• All
UPF, Barcelona, Spain,
2 minutes ago
United States,
2 minutes ago
France,
12 minutes ago
St Louis, MO,
12 minutes ago
Ukraine,
12 minutes ago
Traffic: 821 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6