Showing : Coverage • reset
0
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2
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314
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 7 weeks ago by • 0 • written 10 weeks ago by • 0
2
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4
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338
views
Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
7 months ago Rui • 0
0
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2
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258
views
AlignmentsTrack empty plot
Coverage RNASeq plot Gviz
9 months ago karlaarz • 0
0
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0
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226
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
18 months ago David • 0
0
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1
reply
314
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
22 months ago akhaira • 0
1
vote
2
replies
962
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 2.6 years ago by 11k • written 5.1 years ago by ▴ 10
0
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3
replies
577
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
3.6 years ago faramer86 • 0
0
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1
reply
500
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 4.1 years ago by ▴ 120 • written 4.1 years ago by ▴ 10
3
votes
2
replies
1.1k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 4.3 years ago by 15k • written 4.3 years ago by ▴ 10
0
votes
0
replies
611
views
DSS CpG coverage threshold
DSS WGBS coverage
4.6 years ago floriandeckert ▴ 30
0
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1
reply
841
views
Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
wiggleplotr bigwig coverage ngs
updated 4.6 years ago by ▴ 30 • written 4.6 years ago by • 0
0
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1
reply
1.1k
views
Plot per-base-coverage output of a bed file of whole genome
coverage bed
updated 4.8 years ago by 59k • written 4.8 years ago by • 0
2
votes
5
replies
1.2k
views
GOseq: count bias correction variations?
Coverage goseq
updated 5.1 years ago by 45k • written 7.8 years ago by ▴ 40
1
vote
2
replies
921
views
Gviz off-by-one with STAR BAM
gviz off-by-one STAR BAM coverage
updated 5.2 years ago by 25k • written 5.2 years ago by • 0
4
votes
2
replies
1.1k
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 5.3 years ago by • 0 • written 5.3 years ago by ▴ 40
0
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1
reply
827
views
Views with RleLists and IRangesLists
Views genomicalignments IRangesList coverage RleList
updated 5.8 years ago by 15k • written 5.8 years ago by • 0
0
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0
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809
views
RNA-Seq metagene coverage
coverage
5.8 years ago Jake ▴ 90
0
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1
reply
1.1k
views
Efficient coverage calculation with RleList and GRanges
granges Rle coverage View mean
updated 5.9 years ago by 11k • written 5.9 years ago by ▴ 170
6
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3
replies
1.2k
views
how does coverage() works
biostrings coverage rle iranges
6.0 years ago likeeatingpizza ▴ 10
2
votes
6
replies
878
views
Using edgeR with "traditional" coverage data?
edger rnaseq coverage
updated 6.1 years ago by 7.8k • written 6.1 years ago by • 0
0
votes
2
replies
864
views
How to set a negative coverage to ZERO
genomicranges coverage
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
2
votes
3
replies
964
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage s4vectors seqlengths
6.3 years ago liz.ingsimmons ▴ 140
6
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0
replies
1.7k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma
15.8 years ago • updated 6.3 years ago Gordon Smyth 45k
0
votes
2
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1.7k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma Coverage limma
updated 6.3 years ago by 45k • written 15.8 years ago by ▴ 50
0
votes
2
replies
2.9k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 6.8 years ago by • 0 • written 9.1 years ago by ★ 8.2k
1
vote
2
replies
1.4k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 6.9 years ago by 25k • written 6.9 years ago by ▴ 90
0
votes
5
replies
1.4k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
7.1 years ago • updated 7.0 years ago maria.maqueda • 0
5
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3
replies
989
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 7.1 years ago by 15k • written 7.1 years ago by ▴ 10
2
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6
replies
2.1k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 7.1 years ago by 25k • written 7.1 years ago by ▴ 30
0
votes
3
replies
1.8k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 7.2 years ago by • 0 • written 7.7 years ago by ★ 12k
0
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0
replies
986
views
ggbio plot coverage adjusted for library size
Coverage Normalization Coverage Normalization
7.7 years ago Tengfei Yin ▴ 490
1
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2
replies
2.1k
views
"Normalising" GRanges coverage object
Coverage GO Gviz Coverage GO Gviz
updated 7.8 years ago by 7.8k • written 7.8 years ago by ▴ 350
0
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0
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892
views
ggbio plot coverage adjusted for library size
Coverage Coverage
7.9 years ago James W. MacDonald 59k
0
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0
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1.6k
views
problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name
Coverage Annotation rtracklayer Coverage Annotation rtracklayer
7.9 years ago Marco Blanchette ▴ 220
0
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1
reply
2.7k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
8.0 years ago florian.hahne@novartis.com ★ 1.6k
0
votes
2
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1.2k
views
mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 8.0 years ago by ▴ 220 • written 8.0 years ago by ▴ 10
0
votes
6
replies
1.9k
views
Displaying very deep coverage in Gviz
Coverage Gviz Coverage Gviz
updated 8.0 years ago by ★ 1.6k • written 8.0 years ago by ▴ 130
0
votes
0
replies
761
views
viewApply drops feature names; transfer names between lists
Coverage convert Coverage convert
8.1 years ago Chris Seidel ▴ 80
0
votes
5
replies
2.8k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Annotation graph Gviz Coverage Annotation graph Gviz
updated 8.1 years ago by ▴ 130 • written 8.1 years ago by ▴ 350
0
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0
replies
746
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Gviz Coverage Gviz
8.1 years ago Lance Parsons ▴ 130
1
vote
3
replies
2.8k
views
Blast analysis of two sequences in R
Coverage Coverage
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 100
0
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0
replies
3.1k
views
Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
8.1 years ago Dan Tenenbaum ★ 8.2k
0
votes
0
replies
1.0k
views
easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
8.1 years ago Guest User ★ 12k
0
votes
3
replies
1.5k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 8.1 years ago by 15k • written 8.1 years ago by 11k
0
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0
replies
497
views
CIGAR-aware coverage
Coverage GenomicAlignments Coverage GenomicAlignments
8.2 years ago Hervé Pagès 15k
0
votes
8
replies
1.3k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 8.2 years ago by 11k • written 8.2 years ago by ▴ 30
0
votes
6
replies
1.6k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 8.2 years ago by 13k • written 8.2 years ago by ▴ 170
0
votes
1
reply
1.2k
views
[MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Coverage Regression edgeR MEDIPS Coverage Regression edgeR MEDIPS
updated 8.3 years ago by ▴ 220 • written 8.3 years ago by ▴ 10
0
votes
2
replies
1.7k
views
Gviz - Visualize Reads - Color by Presence of Junction?
Coverage Gviz Coverage Gviz
updated 8.4 years ago by ▴ 730 • written 8.4 years ago by ▴ 120
0
votes
1
reply
1.0k
views
ggbio: mirrored coverage plots for +/- strands
Coverage ggbio Coverage ggbio
updated 8.5 years ago by 11k • written 8.5 years ago by ★ 1.7k
50 results • Page 1 of 1
Recent ...
Replies
Answer: ashr vs apeglm for interaction data by Michael Love 36k
Can you show the MA plot for these two analyses? Also for a gene with a large LFC from ashr, can you show plotCounts?
Comment: Robust Multi-array Average could get negative value or not? by Yang Shi • 0
Got the point sir~ Thanks so much!
Comment: Robust Multi-array Average could get negative value or not? by James W. MacDonald 59k
Because it's a small number.
Comment: Robust Multi-array Average could get negative value or not? by Yang Shi • 0
Thanks for your quick reply sir! Could you tell me why 4 which you selected here?
Answer: Robust Multi-array Average could get negative value or not? by James W. MacDonald 59k
After running RMA, your data have been logged, base 2. Any value < 1 will have a negative value. Looking at the data from that GEO submissi…
Votes
Answer: Robust Multi-array Average could get negative value or not?
Answer: Robust Multi-array Average could get negative value or not?
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
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