Showing : coverage • reset
0
votes
2
replies
3.6k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.1 years ago by ▴ 20 • written 2.1 years ago by • 0
3
votes
4
replies
1.0k
views
Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
2.6 years ago Rui ▴ 10
0
votes
4
replies
1.2k
views
AlignmentsTrack empty plot
Coverage RNASeq plot Gviz
updated 15 months ago by 65k • written 2.7 years ago by • 0
0
votes
0
replies
713
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
3.5 years ago David • 0
0
votes
1
reply
913
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
3.8 years ago akhaira • 0
0
votes
3
replies
1.2k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
5.5 years ago faramer86 • 0
0
votes
1
reply
979
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 6.0 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
3
votes
2
replies
1.9k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 6.2 years ago by 16k • written 6.2 years ago by ▴ 10
0
votes
0
replies
1.3k
views
DSS CpG coverage threshold
DSS WGBS coverage
6.5 years ago floriandeckert ▴ 30
0
votes
1
reply
1.6k
views
Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
wiggleplotr bigwig coverage ngs
updated 6.6 years ago by ▴ 30 • written 6.6 years ago by • 0
0
votes
1
reply
1.6k
views
Plot per-base-coverage output of a bed file of whole genome
coverage bed
updated 6.7 years ago by 65k • written 6.7 years ago by • 0
1
vote
2
replies
1.5k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 4.5 years ago by ★ 11k • written 7.1 years ago by ▴ 10
1
vote
2
replies
1.5k
views
Gviz off-by-one with STAR BAM
gviz off-by-one STAR BAM coverage
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
4
votes
2
replies
1.5k
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 7.2 years ago by • 0 • written 7.3 years ago by ▴ 40
0
votes
1
reply
1.3k
views
Views with RleLists and IRangesLists
Views genomicalignments IRangesList coverage RleList
updated 7.8 years ago by 16k • written 7.8 years ago by • 0
0
votes
0
replies
1.3k
views
RNA-Seq metagene coverage
coverage
7.8 years ago Jake ▴ 90
0
votes
1
reply
1.6k
views
Efficient coverage calculation with RleList and GRanges
granges Rle coverage View mean
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ▴ 170
6
votes
3
replies
2.4k
views
how does coverage() works
biostrings coverage rle iranges
7.9 years ago likeeatingpizza ▴ 10
2
votes
6
replies
1.4k
views
Using edgeR with "traditional" coverage data?
edger rnaseq coverage
updated 8.0 years ago by ★ 7.9k • written 8.0 years ago by • 0
0
votes
2
replies
1.3k
views
How to set a negative coverage to ZERO
genomicranges coverage
updated 8.1 years ago by 25k • written 8.1 years ago by • 0
2
votes
3
replies
1.5k
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage s4vectors seqlengths
8.2 years ago liz.ingsimmons ▴ 140
1
vote
2
replies
1.9k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 90
0
votes
5
replies
2.0k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
9.0 years ago maria.maqueda • 0
5
votes
3
replies
1.7k
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 9.0 years ago by 16k • written 9.0 years ago by ▴ 10
2
votes
6
replies
2.8k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 30
0
votes
4
replies
2.6k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 6 months ago by • 0 • written 9.6 years ago by ★ 13k
0
votes
0
replies
1.3k
views
ggbio plot coverage adjusted for library size
Coverage Normalization Coverage Normalization
9.7 years ago Tengfei Yin ▴ 490
1
vote
2
replies
2.6k
views
"Normalising" GRanges coverage object
Coverage GO Gviz Coverage GO Gviz
updated 9.7 years ago by ★ 7.9k • written 9.7 years ago by ▴ 350
2
votes
5
replies
1.9k
views
GOseq: count bias correction variations?
Coverage goseq
updated 7.0 years ago by 50k • written 9.7 years ago by ▴ 40
0
votes
0
replies
1.2k
views
ggbio plot coverage adjusted for library size
Coverage Coverage
9.8 years ago James W. MacDonald 65k
0
votes
0
replies
2.0k
views
problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name
Coverage Annotation rtracklayer Coverage Annotation rtracklayer
9.9 years ago Marco Blanchette ▴ 220
0
votes
2
replies
1.6k
views
mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 9.9 years ago by ▴ 240 • written 9.9 years ago by ▴ 10
0
votes
6
replies
2.6k
views
Displaying very deep coverage in Gviz
Coverage Gviz Coverage Gviz
updated 10.0 years ago by ★ 1.6k • written 10.0 years ago by ▴ 130
0
votes
1
reply
3.1k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
10.0 years ago • updated 9.9 years ago florian.hahne@novartis.com ★ 1.6k
0
votes
0
replies
1.2k
views
viewApply drops feature names; transfer names between lists
Coverage convert Coverage convert
10.0 years ago Chris Seidel ▴ 80
0
votes
5
replies
3.5k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Annotation graph Gviz Coverage Annotation graph Gviz
updated 10.0 years ago by ▴ 130 • written 10.0 years ago by ▴ 350
0
votes
0
replies
1.1k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Gviz Coverage Gviz
10.0 years ago Lance Parsons ▴ 130
1
vote
3
replies
3.9k
views
Blast analysis of two sequences in R
Coverage Coverage
updated 10.0 years ago by 25k • written 10.0 years ago by ▴ 100
0
votes
0
replies
4.0k
views
Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
10.0 years ago Dan Tenenbaum ★ 8.2k
0
votes
0
replies
1.5k
views
easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
10.0 years ago Guest User ★ 13k
1
vote
3
replies
2.2k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 10.1 years ago by 16k • written 10.1 years ago by ★ 11k
0
votes
0
replies
783
views
CIGAR-aware coverage
Coverage GenomicAlignments Coverage GenomicAlignments
10.2 years ago Hervé Pagès 16k
0
votes
8
replies
1.8k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 30
0
votes
6
replies
2.3k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 10.2 years ago by ★ 13k • written 10.2 years ago by ▴ 170
0
votes
1
reply
1.6k
views
[MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Coverage Regression edgeR MEDIPS Coverage Regression edgeR MEDIPS
updated 10.3 years ago by ▴ 240 • written 10.3 years ago by ▴ 10
0
votes
2
replies
2.2k
views
Gviz - Visualize Reads - Color by Presence of Junction?
Coverage Gviz Coverage Gviz
updated 10.4 years ago by ▴ 730 • written 10.4 years ago by ▴ 120
0
votes
1
reply
1.4k
views
ggbio: mirrored coverage plots for +/- strands
Coverage ggbio Coverage ggbio
updated 10.4 years ago by ★ 11k • written 10.4 years ago by ★ 1.7k
0
votes
16
replies
4.1k
views
subset a RleList using GRanges object?
Coverage Cancer IRanges Coverage Cancer IRanges
updated 10.4 years ago by 16k • written 10.4 years ago by ▴ 740
0
votes
1
reply
1.3k
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 10.4 years ago by ▴ 320 • written 10.4 years ago by 50k
0
votes
0
replies
1.2k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
10.4 years ago Nicolas Delhomme ▴ 320
50 results • Page 1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Awards • All
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Popular Question to Bine ▴ 40
Locations • All
France, just now
United Kingdom, just now
France, 7 minutes ago
UPF, Barcelona, Spain, 17 minutes ago
Germany, 19 minutes ago
Traffic: 845 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6