Showing : Coverage • reset
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Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage Gviz sashimi
7 months ago Marco • 0
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2
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5.5k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.1 years ago by ▴ 20 • written 3.2 years ago by • 0
3
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4
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1.5k
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Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
3.6 years ago Rui ▴ 10
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4
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1.8k
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AlignmentsTrack empty plot
Coverage RNASeq plot Gviz
updated 2.3 years ago by 68k • written 3.8 years ago by • 0
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1.1k
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Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
4.5 years ago David • 0
0
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1
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1.3k
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How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
4.8 years ago akhaira • 0
1
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2
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1.9k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 5.6 years ago by ★ 11k • written 8.1 years ago by ▴ 10
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3
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1.5k
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Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
6.6 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 7.0 years ago by ▴ 130 • written 7.0 years ago by ▴ 10
3
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2
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2.3k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 7.2 years ago by 16k • written 7.3 years ago by ▴ 10
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1
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1.8k
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DSS CpG coverage threshold
DSS WGBS coverage
updated 12 months ago by • 0 • written 7.6 years ago by ▴ 30
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1
reply
2.5k
views
Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
wiggleplotr bigwig coverage ngs
updated 7.6 years ago by ▴ 30 • written 7.6 years ago by • 0
0
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1
reply
2.0k
views
Plot per-base-coverage output of a bed file of whole genome
coverage bed
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 10
2
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5
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2.4k
views
GOseq: count bias correction variations?
Coverage goseq
updated 8.1 years ago by 52k • written 10.8 years ago by ▴ 40
1
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2
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1.8k
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Gviz off-by-one with STAR BAM
gviz off-by-one STAR BAM coverage
updated 8.2 years ago by 25k • written 8.2 years ago by • 0
4
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2
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2.0k
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 8.3 years ago by • 0 • written 8.3 years ago by ▴ 40
0
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1
reply
1.6k
views
Views with RleLists and IRangesLists
Views genomicalignments IRangesList coverage RleList
updated 8.8 years ago by 16k • written 8.8 years ago by • 0
0
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0
replies
1.6k
views
RNA-Seq metagene coverage
coverage
8.8 years ago Jake ▴ 90
0
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1
reply
1.9k
views
Efficient coverage calculation with RleList and GRanges
granges Rle coverage View mean
updated 8.9 years ago by ★ 11k • written 8.9 years ago by ▴ 170
6
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3
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3.2k
views
how does coverage() works
biostrings coverage rle iranges
9.0 years ago likeeatingpizza ▴ 10
2
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6
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1.7k
views
Using edgeR with "traditional" coverage data?
edger rnaseq coverage
updated 9.1 years ago by ★ 7.9k • written 9.1 years ago by • 0
0
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2
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1.6k
views
How to set a negative coverage to ZERO
genomicranges coverage
updated 9.1 years ago by 25k • written 9.1 years ago by • 0
2
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3
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1.9k
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage s4vectors seqlengths
9.2 years ago liz.ingsimmons ▴ 140
6
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0
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3.5k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma
18.8 years ago • updated 9.3 years ago Gordon Smyth 52k
0
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2
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2.8k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma Coverage limma
updated 9.3 years ago by 52k • written 18.8 years ago by ▴ 50
0
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2
replies
4.2k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 9.8 years ago by • 0 • written 12.1 years ago by ★ 8.2k
1
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2
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2.3k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 9.9 years ago by 25k • written 9.9 years ago by ▴ 90
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5
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2.5k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
10.0 years ago maria.maqueda • 0
5
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3
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2.1k
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 10.1 years ago by 16k • written 10.1 years ago by ▴ 10
2
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6
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3.2k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 10.1 years ago by 25k • written 10.1 years ago by ▴ 30
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4
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3.1k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 18 months ago by • 0 • written 10.7 years ago by ★ 13k
0
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0
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1.5k
views
ggbio plot coverage adjusted for library size
Coverage Normalization Coverage Normalization
10.7 years ago Tengfei Yin ▴ 490
1
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2
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3.1k
views
"Normalising" GRanges coverage object
Coverage GO Gviz Coverage GO Gviz
updated 10.8 years ago by ★ 7.9k • written 10.8 years ago by ▴ 350
0
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0
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1.4k
views
ggbio plot coverage adjusted for library size
Coverage Coverage
10.9 years ago James W. MacDonald 68k
0
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0
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2.3k
views
problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name
Coverage Annotation rtracklayer Coverage Annotation rtracklayer
10.9 years ago Marco Blanchette ▴ 220
0
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1
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3.4k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
11.0 years ago florian.hahne@novartis.com ★ 1.6k
0
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2
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1.9k
views
mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 11.0 years ago by ▴ 280 • written 11.0 years ago by ▴ 10
0
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6
replies
3.1k
views
Displaying very deep coverage in Gviz
Coverage Gviz Coverage Gviz
updated 11.0 years ago by ★ 1.6k • written 11.0 years ago by ▴ 130
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0
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1.4k
views
viewApply drops feature names; transfer names between lists
Coverage convert Coverage convert
11.0 years ago Chris Seidel ▴ 80
0
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5
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4.1k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Annotation graph Gviz Coverage Annotation graph Gviz
updated 11.0 years ago by ▴ 130 • written 11.0 years ago by ▴ 350
0
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0
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1.3k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Gviz Coverage Gviz
11.0 years ago Lance Parsons ▴ 130
1
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3
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4.4k
views
Blast analysis of two sequences in R
Coverage Coverage
updated 11.1 years ago by 25k • written 11.1 years ago by ▴ 100
0
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0
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4.4k
views
Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
11.1 years ago Dan Tenenbaum ★ 8.2k
0
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0
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1.7k
views
easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
11.1 years ago Guest User ★ 13k
1
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3
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2.5k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 11.1 years ago by 16k • written 11.1 years ago by ★ 11k
0
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0
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953
views
CIGAR-aware coverage
Coverage GenomicAlignments Coverage GenomicAlignments
11.2 years ago Hervé Pagès 16k
0
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8
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2.1k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 11.2 years ago by ★ 11k • written 11.2 years ago by ▴ 30
0
votes
6
replies
2.8k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 11.2 years ago by ★ 13k • written 11.2 years ago by ▴ 170
0
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1
reply
1.9k
views
[MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Coverage Regression edgeR MEDIPS Coverage Regression edgeR MEDIPS
updated 11.3 years ago by ▴ 280 • written 11.3 years ago by ▴ 10
0
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2
replies
2.4k
views
Gviz - Visualize Reads - Color by Presence of Junction?
Coverage Gviz Coverage Gviz
updated 11.4 years ago by ▴ 750 • written 11.4 years ago by ▴ 120
50 results • Page 1 of 1
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Answer: WGCNA coupled with differential expression analysis: question about baseline mod by phylliskeller162 • 0
My reflexes are challenged every time I play [Dinosaur Game][1]! [1]: https://dinosaur-game.io
Answer: blockwiseModule crashes in the end and doesn't generate modules by phylliskeller162 • 0
Crave adrenaline, music, and pixel-perfect jumps? [Geometry Dash][1] delivers it all in one pulse-pounding ride! [1]: https://geomet…
Comment: How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignm by Charles • 0
I am trying this but it is slow. ``` aln2mismatches <- function (gal) { gr <- GRanges(gal) irl <- cigarRangesAlongReferenceSpace(cigar…
Answer: DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change by James W. MacDonald 68k
Yes, you can simply flip the sign of the logFC to reverse the direction of the comparison.
Comment: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k
The argument for annotation_col is meant to be a `data.frame`, not a vector. The hint in the error is that it has the wrong number of dimen…
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Comment: Heatmap of a transformed deseq object with pheatmap
DESeq2: Question about the alpha in summary() and results()
Comment: How to load scRNA-seq data from GEO
limma correction for tumor purity
limma correction for tumor purity
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