Showing : Coverage • reset
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 20 months ago by • 0 • written 21 months ago by • 0
2
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4
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878
views
Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
2.2 years ago Rui • 0
0
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4
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993
views
AlignmentsTrack empty plot
Coverage RNASeq plot Gviz
updated 10 months ago by 64k • written 2.4 years ago by • 0
0
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0
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586
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
3.1 years ago David • 0
0
votes
1
reply
772
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
3.4 years ago akhaira • 0
1
vote
2
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1.4k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 4.2 years ago by 11k • written 6.7 years ago by ▴ 10
0
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3
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1.0k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
5.1 years ago faramer86 • 0
0
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1
reply
876
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 5.6 years ago by ▴ 130 • written 5.6 years ago by ▴ 10
3
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2
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1.7k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 5.8 years ago by 16k • written 5.8 years ago by ▴ 10
0
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0
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1.1k
views
DSS CpG coverage threshold
DSS WGBS coverage
6.2 years ago floriandeckert ▴ 30
0
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1
reply
1.3k
views
Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
wiggleplotr bigwig coverage ngs
updated 6.2 years ago by ▴ 30 • written 6.2 years ago by • 0
0
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1
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1.5k
views
Plot per-base-coverage output of a bed file of whole genome
coverage bed
updated 6.3 years ago by 64k • written 6.3 years ago by • 0
2
votes
5
replies
1.8k
views
GOseq: count bias correction variations?
Coverage goseq
updated 6.7 years ago by 49k • written 9.4 years ago by ▴ 40
1
vote
2
replies
1.4k
views
Gviz off-by-one with STAR BAM
gviz off-by-one STAR BAM coverage
updated 6.7 years ago by 25k • written 6.7 years ago by • 0
4
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2
replies
1.4k
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 6.9 years ago by • 0 • written 6.9 years ago by ▴ 40
0
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1
reply
1.2k
views
Views with RleLists and IRangesLists
Views genomicalignments IRangesList coverage RleList
updated 7.4 years ago by 16k • written 7.4 years ago by • 0
0
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0
replies
1.2k
views
RNA-Seq metagene coverage
coverage
7.4 years ago Jake ▴ 90
0
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1
reply
1.5k
views
Efficient coverage calculation with RleList and GRanges
granges Rle coverage View mean
updated 7.4 years ago by 11k • written 7.4 years ago by ▴ 170
6
votes
3
replies
2.1k
views
how does coverage() works
biostrings coverage rle iranges
7.5 years ago likeeatingpizza ▴ 10
2
votes
6
replies
1.2k
views
Using edgeR with "traditional" coverage data?
edger rnaseq coverage
updated 7.6 years ago by 7.8k • written 7.6 years ago by • 0
0
votes
2
replies
1.2k
views
How to set a negative coverage to ZERO
genomicranges coverage
updated 7.7 years ago by 25k • written 7.7 years ago by • 0
2
votes
3
replies
1.4k
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage s4vectors seqlengths
7.8 years ago liz.ingsimmons ▴ 140
6
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0
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2.5k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma
17.4 years ago • updated 7.9 years ago Gordon Smyth 49k
0
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2
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2.3k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma Coverage limma
updated 7.9 years ago by 49k • written 17.4 years ago by ▴ 50
0
votes
2
replies
3.6k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 8.4 years ago by • 0 • written 10.7 years ago by ★ 8.2k
1
vote
2
replies
1.8k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 90
0
votes
5
replies
1.8k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
8.6 years ago maria.maqueda • 0
5
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3
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1.6k
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 8.7 years ago by 16k • written 8.7 years ago by ▴ 10
2
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6
replies
2.6k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 8.7 years ago by 25k • written 8.7 years ago by ▴ 30
0
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4
replies
2.4k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 6 weeks ago by • 0 • written 9.3 years ago by ★ 12k
0
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0
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1.3k
views
ggbio plot coverage adjusted for library size
Coverage Normalization Coverage Normalization
9.3 years ago Tengfei Yin ▴ 490
1
vote
2
replies
2.5k
views
"Normalising" GRanges coverage object
Coverage GO Gviz Coverage GO Gviz
updated 9.3 years ago by 7.8k • written 9.3 years ago by ▴ 350
0
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0
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1.1k
views
ggbio plot coverage adjusted for library size
Coverage Coverage
9.4 years ago James W. MacDonald 64k
0
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0
replies
1.9k
views
problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name
Coverage Annotation rtracklayer Coverage Annotation rtracklayer
9.5 years ago Marco Blanchette ▴ 220
0
votes
1
reply
3.0k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
9.6 years ago florian.hahne@novartis.com ★ 1.6k
0
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2
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1.5k
views
mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 9.6 years ago by ▴ 240 • written 9.6 years ago by ▴ 10
0
votes
6
replies
2.4k
views
Displaying very deep coverage in Gviz
Coverage Gviz Coverage Gviz
updated 9.6 years ago by ★ 1.6k • written 9.6 years ago by ▴ 130
0
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0
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1.1k
views
viewApply drops feature names; transfer names between lists
Coverage convert Coverage convert
9.6 years ago Chris Seidel ▴ 80
0
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5
replies
3.3k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Annotation graph Gviz Coverage Annotation graph Gviz
updated 9.6 years ago by ▴ 130 • written 9.6 years ago by ▴ 350
0
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0
replies
987
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Gviz Coverage Gviz
9.6 years ago Lance Parsons ▴ 130
1
vote
3
replies
3.7k
views
Blast analysis of two sequences in R
Coverage Coverage
updated 9.6 years ago by 25k • written 9.6 years ago by ▴ 100
0
votes
0
replies
3.6k
views
Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
9.7 years ago Dan Tenenbaum ★ 8.2k
0
votes
0
replies
1.4k
views
easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
9.7 years ago Guest User ★ 12k
1
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3
replies
2.0k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 9.7 years ago by 16k • written 9.7 years ago by 11k
0
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0
replies
701
views
CIGAR-aware coverage
Coverage GenomicAlignments Coverage GenomicAlignments
9.8 years ago Hervé Pagès 16k
0
votes
8
replies
1.7k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 9.8 years ago by 11k • written 9.8 years ago by ▴ 30
0
votes
6
replies
2.1k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 9.8 years ago by 13k • written 9.8 years ago by ▴ 170
0
votes
1
reply
1.5k
views
[MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Coverage Regression edgeR MEDIPS Coverage Regression edgeR MEDIPS
updated 9.9 years ago by ▴ 240 • written 9.9 years ago by ▴ 10
0
votes
2
replies
2.1k
views
Gviz - Visualize Reads - Color by Presence of Junction?
Coverage Gviz Coverage Gviz
updated 10.0 years ago by ▴ 730 • written 10.0 years ago by ▴ 120
0
votes
1
reply
1.3k
views
ggbio: mirrored coverage plots for +/- strands
Coverage ggbio Coverage ggbio
updated 10.0 years ago by 11k • written 10.0 years ago by ★ 1.7k
50 results • Page 1 of 1
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Comment: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k
> Is it okay to apply removeBatchEffect before a limma analysis(limma linear model)? No, it is not ok to apply any batch correction before…
Comment: Correct the batch effect in methylation analysis in R by kyj2226 • 0
Thank you for your response Gordon :) I've already run the code below, just add batch to the limma linear model design <- model.matri…
Answer: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k
You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model. …
Answer: Agilent Microarray Gene Oncology analysis gone wrong by Gordon Smyth 49k
Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…
Comment: Normalised counts from RUVg in RUVSeq by Shaimaa Gamal • 0
Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …
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Answer: Correct the batch effect in methylation analysis in R
Answer: enrichGOgradient color change
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
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