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Showing :
coverage
•
reset
0
votes
0
replies
148
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
958
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
1
vote
2
replies
1.7k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments
splicing
coverage
updated 5.1 years ago by
Michael Lawrence
★ 11k • written 7.7 years ago by
rasi1983
▴ 10
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
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
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
6
votes
0
replies
3.1k
views
BH vs BY in p.adjust + FDR interpretation
Coverage
limma
18.4 years ago • updated 8.9 years ago
Gordon Smyth
52k
0
votes
2
replies
2.6k
views
BH vs BY in p.adjust + FDR interpretation
Coverage
limma
Coverage
limma
updated 8.9 years ago by
Gordon Smyth
52k • written 18.4 years ago by
lemerle@embl.de
▴ 50
0
votes
2
replies
4.0k
views
Bioconductor 2.12 is released
BiocViews
aCGH
SNP
Transcription
Sequencing
Microarray
Coverage
Alignment
Annotation
GO
updated 9.4 years ago by
marksteve952
• 0 • written 11.7 years ago by
Dan Tenenbaum
★ 8.2k
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
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
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
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
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
50 results • Page
1 of 1
Recent ...
Replies
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Aaron Lun
★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable
by
dtzhu337
• 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable
by
Gordon Smyth
52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd
by
liu.n
• 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd
by
joseph.joonsang
• 0
> dim(spe) [1] 19962 425
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
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