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
0
votes
0
replies
149
views
Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage
Gviz
sashimi
8 weeks ago
Marco
• 0
0
votes
2
replies
4.7k
views
Gene body coverage plot
plot
gene
GenomicRanges
Coverage
R
updated 2.7 years ago by
kent.riemondy
▴ 20 • written 2.7 years ago by
svenbioinf
• 0
3
votes
4
replies
1.3k
views
Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage
DESeq2
3.2 years ago
Rui
▴ 10
0
votes
4
replies
1.6k
views
AlignmentsTrack empty plot
Coverage
RNASeq
plot
Gviz
updated 22 months ago by
James W. MacDonald
67k • written 3.3 years ago by
karlaarz
• 0
0
votes
0
replies
959
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage
rtracklayer
4.1 years ago
David
• 0
0
votes
1
reply
1.1k
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph
.cov
wig
biseq
coverage
4.4 years ago
akhaira
• 0
0
votes
3
replies
1.4k
views
Coverage profile comparison
Targeted sequencing
correlation
coverage
euclid
clustering
6.1 years ago
faramer86
• 0
0
votes
1
reply
1.1k
views
coverage QC file mean duplication and "mom" columns
PureCN
coverage
updated 6.6 years ago by
markus.riester
▴ 130 • written 6.6 years ago by
twtoal
▴ 10
3
votes
2
replies
2.1k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug
genomicranges
granges
rlelist
coverage
updated 6.8 years ago by
Hervé Pagès
16k • written 6.8 years ago by
xiaotong.yao23
▴ 10
0
votes
1
reply
1.6k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 6 months ago by
j.gilbert
• 0 • written 7.2 years ago by
floriandeckert
▴ 30
0
votes
1
reply
2.1k
views
Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
wiggleplotr
bigwig
coverage
ngs
updated 7.2 years ago by
kaur.alasoo
▴ 30 • written 7.2 years ago by
borgmichael
• 0
0
votes
1
reply
1.8k
views
Plot per-base-coverage output of a bed file of whole genome
coverage
bed
updated 7.3 years ago by
James W. MacDonald
67k • written 7.3 years ago by
sgupt46
▴ 10
1
vote
2
replies
1.7k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments
splicing
coverage
updated 5.2 years ago by
Michael Lawrence
★ 11k • written 7.7 years ago by
rasi1983
▴ 10
1
vote
2
replies
1.7k
views
Gviz off-by-one with STAR BAM
gviz
off-by-one
STAR
BAM
coverage
updated 7.7 years ago by
Martin Morgan
25k • written 7.7 years ago by
bernt.popp
• 0
4
votes
2
replies
1.8k
views
bamsignals - bamcoverage has no strand-specific option??
BAM
bamsignals
Coverage
updated 7.9 years ago by
helmuth
• 0 • written 7.9 years ago by
gtho123
▴ 40
0
votes
1
reply
1.5k
views
Views with RleLists and IRangesLists
Views
genomicalignments
IRangesList
coverage
RleList
updated 8.4 years ago by
Hervé Pagès
16k • written 8.4 years ago by
ccanchaya
• 0
0
votes
0
replies
1.5k
views
RNA-Seq metagene coverage
coverage
8.4 years ago
Jake
▴ 90
0
votes
1
reply
1.8k
views
Efficient coverage calculation with RleList and GRanges
granges
Rle
coverage
View
mean
updated 8.4 years ago by
Michael Lawrence
★ 11k • written 8.4 years ago by
Christian Ruckert
▴ 170
6
votes
3
replies
2.9k
views
how does coverage() works
biostrings
coverage
rle
iranges
8.5 years ago
likeeatingpizza
▴ 10
2
votes
6
replies
1.6k
views
Using edgeR with "traditional" coverage data?
edger
rnaseq
coverage
updated 8.6 years ago by
Ryan C. Thompson
★ 7.9k • written 8.6 years ago by
bastien.chevreux
• 0
0
votes
2
replies
1.5k
views
How to set a negative coverage to ZERO
genomicranges
coverage
updated 8.7 years ago by
Martin Morgan
25k • written 8.7 years ago by
vanhzh
• 0
2
votes
3
replies
1.7k
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage
s4vectors
seqlengths
8.8 years ago
liz.ingsimmons
▴ 140
1
vote
2
replies
2.1k
views
Does coverage() split exon spanning RNA-seq reads?
coverage
genomicranges
genomicalignments
updated 9.4 years ago by
Martin Morgan
25k • written 9.4 years ago by
Jake
▴ 90
0
votes
5
replies
2.3k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq
RRBS
SAAP-BS
coverage
9.6 years ago
maria.maqueda
• 0
5
votes
3
replies
1.9k
views
Calling coverage on GRanges object yields small negative values
granges
coverage
updated 9.6 years ago by
Hervé Pagès
16k • written 9.6 years ago by
Anya
▴ 10
2
votes
6
replies
3.0k
views
Shrink or Expand RLE
RLE
iranges
granges
coverage
updated 9.7 years ago by
Martin Morgan
25k • written 9.7 years ago by
gen
▴ 30
0
votes
4
replies
3.0k
views
Error using Bsmooth.tstat due to NAs
Coverage
bsseq
updated 13 months ago by
Adam
• 0 • written 10.2 years ago by
Guest User
★ 13k
0
votes
0
replies
1.4k
views
ggbio plot coverage adjusted for library size
Coverage
Normalization
Coverage
Normalization
10.3 years ago
Tengfei Yin
▴ 490
1
vote
2
replies
2.9k
views
"Normalising" GRanges coverage object
Coverage
GO
Gviz
Coverage
GO
Gviz
updated 10.3 years ago by
Ryan C. Thompson
★ 7.9k • written 10.3 years ago by
Aliaksei Holik
▴ 350
2
votes
5
replies
2.2k
views
GOseq: count bias correction variations?
Coverage
goseq
updated 7.6 years ago by
Gordon Smyth
52k • written 10.4 years ago by
Christopher Conley
▴ 40
0
votes
0
replies
1.3k
views
ggbio plot coverage adjusted for library size
Coverage
Coverage
10.4 years ago
James W. MacDonald
67k
0
votes
0
replies
2.1k
views
problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name
Coverage
Annotation
rtracklayer
Coverage
Annotation
rtracklayer
10.5 years ago
Marco Blanchette
▴ 220
0
votes
2
replies
1.8k
views
mr.edgeR tests in MEDIPS package
Coverage
MEDIPS
Coverage
MEDIPS
updated 10.6 years ago by
Matthias Lienhard
▴ 280 • written 10.6 years ago by
Vining, Kelly
▴ 10
0
votes
6
replies
2.9k
views
Displaying very deep coverage in Gviz
Coverage
Gviz
Coverage
Gviz
updated 10.6 years ago by
florian.hahne@novartis.com
★ 1.6k • written 10.6 years ago by
Lance Parsons
▴ 130
0
votes
1
reply
3.3k
views
displaying coverage RNAseq Gviz
RNASeq
Coverage
Gviz
RNASeq
Coverage
Gviz
10.6 years ago
florian.hahne@novartis.com
★ 1.6k
0
votes
0
replies
1.3k
views
viewApply drops feature names; transfer names between lists
Coverage
convert
Coverage
convert
10.6 years ago
Chris Seidel
▴ 80
0
votes
5
replies
3.8k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage
Annotation
graph
Gviz
Coverage
Annotation
graph
Gviz
updated 10.6 years ago by
Lance Parsons
▴ 130 • written 10.6 years ago by
Aliaksei Holik
▴ 350
0
votes
0
replies
1.2k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage
Gviz
Coverage
Gviz
10.6 years ago
Lance Parsons
▴ 130
1
vote
3
replies
4.2k
views
Blast analysis of two sequences in R
Coverage
Coverage
updated 10.6 years ago by
Martin Morgan
25k • written 10.6 years ago by
prabhakar ghorpade
▴ 100
0
votes
0
replies
4.3k
views
Bioconductor 2.14 is released
BiocViews
aCGH
SNP
Sequencing
RNASeq
ChIPSeq
miRNA
Microarray
qPCR
Metabolomics
Coverage
10.6 years ago
Dan Tenenbaum
★ 8.2k
0
votes
0
replies
1.6k
views
easyRNASeq: Number of total counts
GeneExpression
RNASeq
Genetics
Coverage
Normalization
BSgenome
Biobase
Biostrings
biomaRt
10.7 years ago
Guest User
★ 13k
1
vote
3
replies
2.4k
views
views on Rle using GRanges object
RNASeq
Coverage
GO
Cancer
bridge
rtracklayer
IRanges
RNASeq
Coverage
GO
Cancer
bridge
updated 10.7 years ago by
Hervé Pagès
16k • written 10.7 years ago by
Michael Lawrence
★ 11k
0
votes
0
replies
888
views
CIGAR-aware coverage
Coverage
GenomicAlignments
Coverage
GenomicAlignments
10.8 years ago
Hervé Pagès
16k
0
votes
8
replies
2.0k
views
CIGAR-aware coverage
Coverage
IRanges
Coverage
IRanges
updated 10.8 years ago by
Michael Lawrence
★ 11k • written 10.8 years ago by
chris warth
▴ 30
0
votes
6
replies
2.6k
views
Gviz: axes related parameters
Coverage
Gviz
Coverage
Gviz
updated 10.8 years ago by
Steve Lianoglou
★ 13k • written 10.8 years ago by
Maxim
▴ 170
0
votes
1
reply
1.8k
views
[MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Coverage
Regression
edgeR
MEDIPS
Coverage
Regression
edgeR
MEDIPS
updated 10.9 years ago by
Matthias Lienhard
▴ 280 • written 10.9 years ago by
Pierre Lindenbaum
▴ 10
0
votes
2
replies
2.3k
views
Gviz - Visualize Reads - Color by Presence of Junction?
Coverage
Gviz
Coverage
Gviz
updated 11.0 years ago by
Robert Ivanek
▴ 750 • written 11.0 years ago by
Andrew Jaffe
▴ 120
0
votes
1
reply
1.6k
views
ggbio: mirrored coverage plots for +/- strands
Coverage
ggbio
Coverage
ggbio
updated 11.0 years ago by
Michael Lawrence
★ 11k • written 11.0 years ago by
Thomas Girke
★ 1.7k
0
votes
16
replies
4.4k
views
subset a RleList using GRanges object?
Coverage
Cancer
IRanges
Coverage
Cancer
IRanges
updated 11.0 years ago by
Hervé Pagès
16k • written 11.0 years ago by
Janet Young
▴ 740
0
votes
1
reply
1.5k
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 11.0 years ago by
Nicolas Delhomme
▴ 320 • written 11.0 years ago by
Gordon Smyth
52k
50 results • Page
1 of 1
Recent ...
Replies
Comment: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Aaron Lun
★ 28k
You can examine the structure of a `DelayedMatrix` by calling the `showtree()` function. For example: ``` library(scRNAseq) X <- fetchData…
Comment: lfcShrink and alpha value
by
cropero
• 0
Thank you so much! Would that be equivalent to perform `res <- results(dds, contrast = c("conditions", "wild_type_114_2_no_carbon", "wild_t…
Comment: pathview - multiple states
by
Philippine
• 0
Thank you! Here a subset of genes that really works with "ame04145". data <- data.frame( EntrezID = c(100577548, 100577764, 406…
Comment: pathview - multiple states
by
Guido Hooiveld
★ 4.1k
A quick comment after I copied/pasted your code: when using `geneList1` in the 3rd code chunk I do **not** get a nice plot... I rather got …
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Adam
• 0
Hi Aaron, Thanks a lot for your help! As you mentioned, I checked my data and it is "DelayedMatrix". I don't know the detailed differe…
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
Awards
• All
Popular Question
to
tombate94
• 0
Popular Question
to
Ou, Jianhong
★ 1.3k
Popular Question
to
mikat
• 0
Popular Question
to
joseph.joonsang
• 0
Popular Question
to
Hans-Ulrich Klein
▴ 330
Locations
• All
WEHI, Melbourne, Australia,
18 minutes ago
The city by the bay,
21 minutes ago
France,
28 minutes ago
Australia,
1 hour ago
United Kingdom,
1 hour ago
Traffic: 550 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