Showing : coverage • reset
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179
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Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage Gviz sashimi
3 months ago Marco • 0
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2
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4.8k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.8 years ago by ▴ 20 • written 2.8 years ago by • 0
3
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4
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1.3k
views
Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
3.3 years ago Rui ▴ 10
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4
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1.6k
views
AlignmentsTrack empty plot
Coverage RNASeq plot Gviz
updated 23 months ago by 67k • written 3.4 years ago by • 0
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0
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984
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Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
4.2 years ago David • 0
0
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1
reply
1.2k
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
4.5 years ago akhaira • 0
1
vote
2
replies
1.8k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 5.2 years ago by ★ 11k • written 7.8 years ago by ▴ 10
0
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3
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1.4k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
6.2 years ago faramer86 • 0
0
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1
reply
1.2k
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by ▴ 10
3
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2
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2.1k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 6.9 years ago by 16k • written 6.9 years ago by ▴ 10
0
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1
reply
1.6k
views
DSS CpG coverage threshold
DSS WGBS coverage
updated 8 months ago by • 0 • written 7.2 years ago by ▴ 30
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1
reply
2.2k
views
Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
wiggleplotr bigwig coverage ngs
updated 7.3 years ago by ▴ 30 • written 7.3 years ago by • 0
0
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1
reply
1.9k
views
Plot per-base-coverage output of a bed file of whole genome
coverage bed
updated 7.4 years ago by 67k • written 7.4 years ago by ▴ 10
2
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5
replies
2.2k
views
GOseq: count bias correction variations?
Coverage goseq
updated 7.7 years ago by 52k • written 10.5 years ago by ▴ 40
1
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2
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1.7k
views
Gviz off-by-one with STAR BAM
gviz off-by-one STAR BAM coverage
updated 7.8 years ago by 25k • written 7.8 years ago by • 0
4
votes
2
replies
1.8k
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 8.0 years ago by • 0 • written 8.0 years ago by ▴ 40
0
votes
1
reply
1.5k
views
Views with RleLists and IRangesLists
Views genomicalignments IRangesList coverage RleList
updated 8.5 years ago by 16k • written 8.5 years ago by • 0
0
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0
replies
1.5k
views
RNA-Seq metagene coverage
coverage
8.5 years ago Jake ▴ 90
0
votes
1
reply
1.8k
views
Efficient coverage calculation with RleList and GRanges
granges Rle coverage View mean
updated 8.5 years ago by ★ 11k • written 8.5 years ago by ▴ 170
6
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3
replies
3.0k
views
how does coverage() works
biostrings coverage rle iranges
8.6 years ago likeeatingpizza ▴ 10
2
votes
6
replies
1.6k
views
Using edgeR with "traditional" coverage data?
edger rnaseq coverage
updated 8.7 years ago by ★ 7.9k • written 8.7 years ago by • 0
0
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2
replies
1.5k
views
How to set a negative coverage to ZERO
genomicranges coverage
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
2
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3
replies
1.8k
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage s4vectors seqlengths
8.9 years ago liz.ingsimmons ▴ 140
6
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0
replies
3.2k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma
18.5 years ago • updated 9.0 years ago Gordon Smyth 52k
0
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2
replies
2.6k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma Coverage limma
updated 9.0 years ago by 52k • written 18.5 years ago by ▴ 50
0
votes
2
replies
4.1k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 9.5 years ago by • 0 • written 11.8 years ago by ★ 8.2k
1
vote
2
replies
2.1k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 9.5 years ago by 25k • written 9.5 years ago by ▴ 90
0
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5
replies
2.3k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
9.7 years ago maria.maqueda • 0
5
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3
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2.0k
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 10
2
votes
6
replies
3.0k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 9.8 years ago by 25k • written 9.8 years ago by ▴ 30
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4
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3.0k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 14 months ago by • 0 • written 10.3 years ago by ★ 13k
0
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0
replies
1.4k
views
ggbio plot coverage adjusted for library size
Coverage Normalization Coverage Normalization
10.4 years ago Tengfei Yin ▴ 490
1
vote
2
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3.0k
views
"Normalising" GRanges coverage object
Coverage GO Gviz Coverage GO Gviz
updated 10.4 years ago by ★ 7.9k • written 10.4 years ago by ▴ 350
0
votes
0
replies
1.3k
views
ggbio plot coverage adjusted for library size
Coverage Coverage
10.5 years ago James W. MacDonald 67k
0
votes
0
replies
2.2k
views
problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name
Coverage Annotation rtracklayer Coverage Annotation rtracklayer
10.6 years ago Marco Blanchette ▴ 220
0
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1
reply
3.3k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
10.7 years ago • updated 10.6 years ago florian.hahne@novartis.com ★ 1.6k
0
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2
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1.8k
views
mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 10.6 years ago by ▴ 280 • written 10.7 years ago by ▴ 10
0
votes
6
replies
2.9k
views
Displaying very deep coverage in Gviz
Coverage Gviz Coverage Gviz
updated 10.7 years ago by ★ 1.6k • written 10.7 years ago by ▴ 130
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0
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1.3k
views
viewApply drops feature names; transfer names between lists
Coverage convert Coverage convert
10.7 years ago Chris Seidel ▴ 80
0
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5
replies
3.9k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Annotation graph Gviz Coverage Annotation graph Gviz
updated 10.7 years ago by ▴ 130 • written 10.7 years ago by ▴ 350
0
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0
replies
1.2k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Gviz Coverage Gviz
10.7 years ago Lance Parsons ▴ 130
1
vote
3
replies
4.2k
views
Blast analysis of two sequences in R
Coverage Coverage
updated 10.7 years ago by 25k • written 10.7 years ago by ▴ 100
0
votes
0
replies
4.3k
views
Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
10.7 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
10.8 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 10.8 years ago by 16k • written 10.8 years ago by ★ 11k
0
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0
replies
903
views
CIGAR-aware coverage
Coverage GenomicAlignments Coverage GenomicAlignments
10.9 years ago Hervé Pagès 16k
0
votes
8
replies
2.0k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 10.9 years ago by ★ 11k • written 10.9 years ago by ▴ 30
0
votes
6
replies
2.6k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 10.9 years ago by ★ 13k • written 10.9 years ago by ▴ 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 11.0 years ago by ▴ 280 • written 11.0 years ago by ▴ 10
0
votes
2
replies
2.3k
views
Gviz - Visualize Reads - Color by Presence of Junction?
Coverage Gviz Coverage Gviz
updated 11.1 years ago by ▴ 750 • written 11.1 years ago by ▴ 120
50 results • Page 1 of 1
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Comment: Package `not available for Bioconductor version '3.20'` when it should be by Levi Waldron ★ 1.1k
Thanks, @mike-smith . I'll let the maintainer @bhaibeka know.
Answer: Package `not available for Bioconductor version '3.20'` when it should be by Mike Smith ★ 6.6k
Copy/paste of a similar answer I gave in the past - hopefully I updated all the package names. TL;DR The **genefu** package is failing to …
Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0
So I changed it to ~0 + group (with the same plot), but I still don't know if it's good or what to fix if not.
Answer: Newbie Question - adding metadata to an analysis by James W. MacDonald 67k
See [Section 4][1]. But do note that you do not need for the `phenoData` slot to contain the data. You can simply have a 'targets' data.fra…
Comment: Want numbers in DESeq to be seen as numerical, not categorical by swbarnes2 ★ 1.4k
How did you import the data? Did you accidently leave in `stringAsFactors=True`? But I'm not entirely sure that you don't want that to be…
Votes
Answer: Package `not available for Bioconductor version '3.20'` when it should be
Comment: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
Comment: Theoretical WGCNA Question
Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a
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