Showing : Coverage • reset
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Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage Gviz sashimi
updated 4 months ago by • 0 • written 12 months ago by • 0
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2
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5.9k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.5 years ago by ▴ 20 • written 3.6 years ago by • 0
3
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4
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1.6k
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Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
4.0 years ago Rui ▴ 10
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4
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1.9k
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AlignmentsTrack empty plot
Coverage RNASeq plot Gviz
updated 2.7 years ago by 68k • written 4.2 years ago by • 0
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1.2k
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Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
4.9 years ago David • 0
0
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1
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1.4k
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
5.2 years ago akhaira • 0
1
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2
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2.0k
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Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 6.0 years ago by ★ 11k • written 8.5 years ago by ▴ 10
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3
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1.7k
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Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
7.0 years ago faramer86 • 0
0
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1
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1.3k
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 7.4 years ago by ▴ 130 • written 7.4 years ago by ▴ 10
3
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2
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2.4k
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coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 7.7 years ago by 16k • written 7.7 years ago by ▴ 10
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1
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1.9k
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DSS CpG coverage threshold
DSS WGBS coverage
updated 17 months ago by • 0 • written 8.0 years ago by ▴ 30
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1
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2.7k
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Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
wiggleplotr bigwig coverage ngs
updated 8.0 years ago by ▴ 30 • written 8.0 years ago by • 0
0
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1
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2.0k
views
Plot per-base-coverage output of a bed file of whole genome
coverage bed
updated 8.2 years ago by 68k • written 8.2 years ago by ▴ 10
2
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5
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2.5k
views
GOseq: count bias correction variations?
Coverage goseq
updated 8.5 years ago by 53k • written 11.2 years ago by ▴ 40
1
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2
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1.9k
views
Gviz off-by-one with STAR BAM
gviz off-by-one STAR BAM coverage
updated 8.6 years ago by 25k • written 8.6 years ago by • 0
4
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2
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2.1k
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bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 8.7 years ago by • 0 • written 8.7 years ago by ▴ 40
0
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1
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1.7k
views
Views with RleLists and IRangesLists
Views genomicalignments IRangesList coverage RleList
updated 9.2 years ago by 16k • written 9.2 years ago by • 0
0
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0
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1.7k
views
RNA-Seq metagene coverage
coverage
9.2 years ago Jake ▴ 90
0
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1
reply
2.0k
views
Efficient coverage calculation with RleList and GRanges
granges Rle coverage View mean
updated 9.3 years ago by ★ 11k • written 9.3 years ago by ▴ 170
6
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3
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3.4k
views
how does coverage() works
biostrings coverage rle iranges
9.4 years ago likeeatingpizza ▴ 10
2
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6
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1.9k
views
Using edgeR with "traditional" coverage data?
edger rnaseq coverage
updated 9.5 years ago by ★ 7.9k • written 9.5 years ago by • 0
0
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2
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1.7k
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How to set a negative coverage to ZERO
genomicranges coverage
updated 9.5 years ago by 25k • written 9.5 years ago by • 0
2
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3
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2.0k
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage s4vectors seqlengths
9.6 years ago liz.ingsimmons ▴ 140
6
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0
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3.6k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma
19.2 years ago • updated 9.7 years ago Gordon Smyth 53k
0
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2
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2.9k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma Coverage limma
updated 9.7 years ago by 53k • written 19.2 years ago by ▴ 50
0
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2
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4.3k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 10.2 years ago by • 0 • written 12.5 years ago by ★ 8.2k
1
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2
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2.4k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 10.3 years ago by 25k • written 10.3 years ago by ▴ 90
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5
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2.6k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
10.5 years ago • updated 10.4 years ago maria.maqueda • 0
5
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3
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2.2k
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 10.5 years ago by 16k • written 10.5 years ago by ▴ 10
2
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6
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3.3k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 10.5 years ago by 25k • written 10.5 years ago by ▴ 30
0
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4
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3.3k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 23 months ago by • 0 • written 11.1 years ago by ★ 13k
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0
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1.6k
views
ggbio plot coverage adjusted for library size
Coverage Normalization Coverage Normalization
11.1 years ago Tengfei Yin ▴ 490
1
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2
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3.3k
views
"Normalising" GRanges coverage object
Coverage GO Gviz Coverage GO Gviz
updated 11.2 years ago by ★ 7.9k • written 11.2 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
11.3 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
11.3 years ago Marco Blanchette ▴ 220
0
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1
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3.5k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
11.4 years ago florian.hahne@novartis.com ★ 1.6k
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2
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2.0k
views
mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 11.4 years ago by ▴ 280 • written 11.4 years ago by ▴ 10
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6
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3.2k
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Displaying very deep coverage in Gviz
Coverage Gviz Coverage Gviz
updated 11.4 years ago by ★ 1.6k • written 11.4 years ago by ▴ 130
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0
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1.4k
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viewApply drops feature names; transfer names between lists
Coverage convert Coverage convert
11.4 years ago Chris Seidel ▴ 80
0
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5
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4.2k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Annotation graph Gviz Coverage Annotation graph Gviz
updated 11.4 years ago by ▴ 130 • written 11.4 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
11.4 years ago Lance Parsons ▴ 130
1
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3
replies
4.6k
views
Blast analysis of two sequences in R
Coverage Coverage
updated 11.5 years ago by 25k • written 11.5 years ago by ▴ 100
0
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0
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4.5k
views
Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
11.5 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
11.5 years ago Guest User ★ 13k
1
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3
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2.7k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 11.5 years ago by 16k • written 11.5 years ago by ★ 11k
0
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0
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998
views
CIGAR-aware coverage
Coverage GenomicAlignments Coverage GenomicAlignments
11.6 years ago Hervé Pagès 16k
0
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8
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2.3k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 11.6 years ago by ★ 11k • written 11.6 years ago by ▴ 30
0
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6
replies
3.0k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ▴ 170
0
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1
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2.0k
views
[MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Coverage Regression edgeR MEDIPS Coverage Regression edgeR MEDIPS
updated 11.7 years ago by ▴ 280 • written 11.7 years ago by ▴ 10
0
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2
replies
2.5k
views
Gviz - Visualize Reads - Color by Presence of Junction?
Coverage Gviz Coverage Gviz
updated 11.8 years ago by ▴ 750 • written 11.8 years ago by ▴ 120
152 results • Page 1 of 4
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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