Showing : Coverage • reset
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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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4.9k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.8 years ago by ▴ 20 • written 2.9 years ago by • 0
3
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4
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1.3k
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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 2.0 years ago by 67k • written 3.5 years ago by • 0
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0
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994
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Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
4.2 years ago David • 0
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1
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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
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2
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1.8k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 5.3 years ago by ★ 11k • written 7.8 years ago by ▴ 10
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3
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1.4k
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Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
6.3 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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2.2k
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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
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1
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1.6k
views
DSS CpG coverage threshold
DSS WGBS coverage
updated 8 months ago by • 0 • written 7.3 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
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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 7.5 years ago by ▴ 10
2
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5
replies
2.2k
views
GOseq: count bias correction variations?
Coverage goseq
updated 7.8 years ago by 52k • written 10.5 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 7.9 years ago by 25k • written 7.9 years ago by • 0
4
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2
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1.9k
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
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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
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1.5k
views
RNA-Seq metagene coverage
coverage
8.5 years ago Jake ▴ 90
0
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1
reply
1.8k
views
Efficient coverage calculation with RleList and GRanges
granges Rle coverage View mean
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ▴ 170
6
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3
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3.0k
views
how does coverage() works
biostrings coverage rle iranges
8.6 years ago likeeatingpizza ▴ 10
2
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6
replies
1.6k
views
Using edgeR with "traditional" coverage data?
edger rnaseq coverage
updated 8.8 years ago by ★ 7.9k • written 8.8 years ago by • 0
0
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2
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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
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1.8k
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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
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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
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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
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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
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2
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2.2k
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
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5
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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 9.8 years ago by 16k • written 9.8 years ago by ▴ 10
2
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6
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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 15 months ago by • 0 • written 10.4 years ago by ★ 13k
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0
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1.5k
views
ggbio plot coverage adjusted for library size
Coverage Normalization Coverage Normalization
10.4 years ago Tengfei Yin ▴ 490
1
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2
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3.0k
views
"Normalising" GRanges coverage object
Coverage GO Gviz Coverage GO Gviz
updated 10.5 years ago by ★ 7.9k • written 10.5 years ago by ▴ 350
0
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0
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1.3k
views
ggbio plot coverage adjusted for library size
Coverage Coverage
10.5 years ago James W. MacDonald 67k
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0
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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
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3.3k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
10.7 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 10.7 years ago by ▴ 280 • written 10.7 years ago by ▴ 10
0
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6
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3.0k
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
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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
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1.2k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Gviz Coverage Gviz
10.7 years ago Lance Parsons ▴ 130
1
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3
replies
4.2k
views
Blast analysis of two sequences in R
Coverage Coverage
updated 10.8 years ago by 25k • written 10.8 years ago by ▴ 100
0
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0
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4.3k
views
Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
10.8 years ago Dan Tenenbaum ★ 8.2k
0
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0
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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
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3
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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
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907
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
2.7k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 10.9 years ago by ★ 13k • written 10.9 years ago by ▴ 170
0
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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
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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
Recent ...
Replies
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 740
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
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