Showing : coverage • reset
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105
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Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
8 months ago David • 0
0
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1
reply
157
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
12 months ago akhaira • 0
1
vote
2
replies
807
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 21 months ago by 11k • written 4.3 years ago by ▴ 10
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3
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438
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
2.8 years ago faramer86 • 0
0
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1
reply
385
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 3.2 years ago by ▴ 110 • written 3.2 years ago by • 0
3
votes
2
replies
869
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 3.5 years ago by 15k • written 3.5 years ago by ▴ 10
0
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0
replies
510
views
DSS CpG coverage threshold
DSS WGBS coverage
3.8 years ago floriandeckert ▴ 30
0
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1
reply
663
views
Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
wiggleplotr bigwig coverage ngs
updated 3.8 years ago by ▴ 30 • written 3.8 years ago by • 0
0
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1
reply
941
views
Plot per-base-coverage output of a bed file of whole genome
coverage bed
updated 4.0 years ago by 57k • written 4.0 years ago by • 0
2
votes
5
replies
1.0k
views
GOseq: count bias correction variations?
Coverage goseq
updated 4.3 years ago by 43k • written 7.0 years ago by ▴ 40
1
vote
2
replies
770
views
Gviz off-by-one with STAR BAM
gviz off-by-one STAR BAM coverage
updated 4.4 years ago by 25k • written 4.4 years ago by • 0
4
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2
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892
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 4.5 years ago by • 0 • written 4.5 years ago by ▴ 40
0
votes
1
reply
705
views
Views with RleLists and IRangesLists
Views genomicalignments IRangesList coverage RleList
updated 5.0 years ago by 15k • written 5.0 years ago by • 0
0
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0
replies
677
views
RNA-Seq metagene coverage
coverage
5.0 years ago Jake ▴ 90
0
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1
reply
998
views
Efficient coverage calculation with RleList and GRanges
granges Rle coverage View mean
updated 5.1 years ago by 11k • written 5.1 years ago by ▴ 170
6
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3
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951
views
how does coverage() works
biostrings coverage rle iranges
5.2 years ago likeeatingpizza • 0
2
votes
6
replies
784
views
Using edgeR with "traditional" coverage data?
edger rnaseq coverage
updated 5.3 years ago by 7.6k • written 5.3 years ago by • 0
0
votes
2
replies
780
views
How to set a negative coverage to ZERO
genomicranges coverage
updated 5.3 years ago by 25k • written 5.3 years ago by • 0
2
votes
3
replies
814
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage s4vectors seqlengths
5.5 years ago liz.ingsimmons ▴ 140
6
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0
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1.4k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma
15.0 years ago • updated 5.5 years ago Gordon Smyth 43k
0
votes
2
replies
1.6k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma Coverage limma
updated 5.5 years ago by 43k • written 15.0 years ago by ▴ 50
0
votes
2
replies
2.5k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 6.0 years ago by • 0 • written 8.3 years ago by ★ 8.2k
1
vote
2
replies
1.3k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 90
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5
replies
1.2k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
6.3 years ago • updated 6.2 years ago maria.maqueda • 0
5
votes
3
replies
874
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 6.3 years ago by 15k • written 6.3 years ago by ▴ 10
2
votes
6
replies
1.9k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 6.3 years ago by 25k • written 6.3 years ago by ▴ 30
0
votes
3
replies
1.5k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 6.4 years ago by • 0 • written 6.9 years ago by ★ 12k
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0
replies
889
views
ggbio plot coverage adjusted for library size
Coverage Normalization Coverage Normalization
6.9 years ago Tengfei Yin ▴ 490
1
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2
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1.8k
views
"Normalising" GRanges coverage object
Coverage GO Gviz Coverage GO Gviz
updated 7.0 years ago by 7.6k • written 7.0 years ago by ▴ 350
0
votes
0
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820
views
ggbio plot coverage adjusted for library size
Coverage Coverage
7.1 years ago James W. MacDonald 57k
0
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0
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1.5k
views
problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name
Coverage Annotation rtracklayer Coverage Annotation rtracklayer
7.1 years ago Marco Blanchette ▴ 220
0
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1
reply
2.5k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
7.2 years ago florian.hahne@novartis.com ★ 1.6k
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2
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1.0k
views
mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 7.2 years ago by ▴ 220 • written 7.2 years ago by ▴ 10
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6
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1.7k
views
Displaying very deep coverage in Gviz
Coverage Gviz Coverage Gviz
updated 7.2 years ago by ★ 1.6k • written 7.2 years ago by ▴ 130
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0
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676
views
viewApply drops feature names; transfer names between lists
Coverage convert Coverage convert
7.2 years ago Chris Seidel ▴ 80
0
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5
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2.6k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Annotation graph Gviz Coverage Annotation graph Gviz
updated 7.3 years ago by ▴ 130 • written 7.3 years ago by ▴ 350
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0
replies
678
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Gviz Coverage Gviz
7.3 years ago Lance Parsons ▴ 130
1
vote
3
replies
2.5k
views
Blast analysis of two sequences in R
Coverage Coverage
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 100
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0
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2.9k
views
Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
7.3 years ago Dan Tenenbaum ★ 8.2k
0
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0
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927
views
easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
7.3 years ago Guest User ★ 12k
0
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3
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1.3k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 7.3 years ago by 15k • written 7.3 years ago by 11k
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0
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440
views
CIGAR-aware coverage
Coverage GenomicAlignments Coverage GenomicAlignments
7.4 years ago Hervé Pagès 15k
0
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8
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1.1k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 7.4 years ago by 11k • written 7.4 years ago by ▴ 30
0
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6
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1.5k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 7.4 years ago by 13k • written 7.4 years ago by ▴ 170
0
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1
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1.1k
views
[MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Coverage Regression edgeR MEDIPS Coverage Regression edgeR MEDIPS
updated 7.5 years ago by ▴ 220 • written 7.5 years ago by ▴ 10
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2
replies
1.6k
views
Gviz - Visualize Reads - Color by Presence of Junction?
Coverage Gviz Coverage Gviz
updated 7.6 years ago by ▴ 680 • written 7.6 years ago by ▴ 120
0
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1
reply
925
views
ggbio: mirrored coverage plots for +/- strands
Coverage ggbio Coverage ggbio
updated 7.6 years ago by 11k • written 7.6 years ago by ★ 1.7k
0
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16
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2.8k
views
subset a RleList using GRanges object?
Coverage Cancer IRanges Coverage Cancer IRanges
updated 7.7 years ago by 15k • written 7.7 years ago by ▴ 740
0
votes
1
reply
834
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges Rsubread easyRNASeq GO
updated 7.7 years ago by ▴ 320 • written 7.7 years ago by 43k
0
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0
replies
814
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
7.7 years ago Nicolas Delhomme ▴ 320
50 results • Page 1 of 1
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Comment: WGCNA adjust p value by Kevin Blighe 3.2k
Cross-posted: https://www.biostars.org/p/9482927/
Comment: Unique GPos taking into account mcols by Marcel Ramos 540
Hi @maltethodberg We currently do not have a method that does this. Perhaps a `duplicated` method is appropriate but I am not the develop…
Comment: What are these genes ? [How to get Ensembl IDs for them] by abf ▴ 30
Mouse genes are not typically all capitals, but I was able to find a reference to a mouse gene in NCBI to [CH36-217G15][1]. Maybe this is …
Comment: Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db. by abf ▴ 30
I should note that when I query org.Mm.eg.db using the gene Symbols associated with my differential expression data I find a 1:1 correspond…
Comment: Best practice for quantifying sncRNA by James W. MacDonald 57k
That question is about GeneGlobe, which is a Qiagen product. I would recommend going to their site and figuring out for yourself.
Votes
A: Finding orthologous human/mouse ENSEMBL IDs
Comment: What are these genes ? [How to get Ensembl IDs for them]
Answer: What lfcSE is dependent upon?
Comment: P value and Adj. P value showing N/A
Answer: P value and Adj. P value showing N/A
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