Showing : coverage • reset
2
votes
4
replies
286
views
Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
3 months ago Rui • 0
0
votes
2
replies
197
views
AlignmentsTrack empty plot
Coverage RNASeq plot Gviz
5 months ago karlaarz • 0
0
votes
0
replies
188
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
14 months ago David • 0
0
votes
1
reply
264
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
18 months ago akhaira • 0
1
vote
2
replies
903
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 2.3 years ago by 11k • written 4.8 years ago by ▴ 10
0
votes
3
replies
533
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
3.3 years ago faramer86 • 0
0
votes
1
reply
463
views
coverage QC file mean duplication and "mom" columns
PureCN coverage
updated 3.7 years ago by ▴ 120 • written 3.7 years ago by ▴ 10
3
votes
2
replies
997
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 3.9 years ago by 15k • written 3.9 years ago by ▴ 10
0
votes
0
replies
575
views
DSS CpG coverage threshold
DSS WGBS coverage
4.3 years ago floriandeckert ▴ 30
0
votes
1
reply
773
views
Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
wiggleplotr bigwig coverage ngs
updated 4.3 years ago by ▴ 30 • written 4.3 years ago by • 0
0
votes
1
reply
1.1k
views
Plot per-base-coverage output of a bed file of whole genome
coverage bed
updated 4.4 years ago by 58k • written 4.4 years ago by • 0
2
votes
5
replies
1.1k
views
GOseq: count bias correction variations?
Coverage goseq
updated 4.8 years ago by 44k • written 7.5 years ago by ▴ 40
1
vote
2
replies
868
views
Gviz off-by-one with STAR BAM
gviz off-by-one STAR BAM coverage
updated 4.8 years ago by 25k • written 4.9 years ago by • 0
4
votes
2
replies
1.0k
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 5.0 years ago by • 0 • written 5.0 years ago by ▴ 40
0
votes
1
reply
785
views
Views with RleLists and IRangesLists
Views genomicalignments IRangesList coverage RleList
updated 5.5 years ago by 15k • written 5.5 years ago by • 0
0
votes
0
replies
740
views
RNA-Seq metagene coverage
coverage
5.5 years ago Jake ▴ 90
0
votes
1
reply
1.1k
views
Efficient coverage calculation with RleList and GRanges
granges Rle coverage View mean
updated 5.5 years ago by 11k • written 5.5 years ago by ▴ 170
6
votes
3
replies
1.1k
views
how does coverage() works
biostrings coverage rle iranges
5.6 years ago likeeatingpizza ▴ 10
2
votes
6
replies
843
views
Using edgeR with "traditional" coverage data?
edger rnaseq coverage
updated 5.8 years ago by 7.7k • written 5.8 years ago by • 0
0
votes
2
replies
832
views
How to set a negative coverage to ZERO
genomicranges coverage
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
2
votes
3
replies
927
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage s4vectors seqlengths
5.9 years ago liz.ingsimmons ▴ 140
6
votes
0
replies
1.6k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma
15.5 years ago • updated 6.0 years ago Gordon Smyth 44k
0
votes
2
replies
1.7k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma Coverage limma
updated 6.0 years ago by 44k • written 15.5 years ago by ▴ 50
0
votes
2
replies
2.7k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 6.5 years ago by • 0 • written 8.8 years ago by ★ 8.2k
1
vote
2
replies
1.4k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 90
0
votes
5
replies
1.3k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
6.7 years ago maria.maqueda • 0
5
votes
3
replies
946
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 6.8 years ago by 15k • written 6.8 years ago by ▴ 10
2
votes
6
replies
2.0k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 6.8 years ago by 25k • written 6.8 years ago by ▴ 30
0
votes
3
replies
1.7k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 6.9 years ago by • 0 • written 7.4 years ago by ★ 12k
0
votes
0
replies
944
views
ggbio plot coverage adjusted for library size
Coverage Normalization Coverage Normalization
7.4 years ago Tengfei Yin ▴ 490
1
vote
2
replies
2.0k
views
"Normalising" GRanges coverage object
Coverage GO Gviz Coverage GO Gviz
updated 7.5 years ago by 7.7k • written 7.5 years ago by ▴ 350
0
votes
0
replies
867
views
ggbio plot coverage adjusted for library size
Coverage Coverage
7.5 years ago James W. MacDonald 58k
0
votes
0
replies
1.5k
views
problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name
Coverage Annotation rtracklayer Coverage Annotation rtracklayer
7.6 years ago Marco Blanchette ▴ 220
0
votes
1
reply
2.6k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
7.7 years ago florian.hahne@novartis.com ★ 1.6k
0
votes
2
replies
1.1k
views
mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 7.7 years ago by ▴ 220 • written 7.7 years ago by ▴ 10
0
votes
6
replies
1.9k
views
Displaying very deep coverage in Gviz
Coverage Gviz Coverage Gviz
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by ▴ 130
0
votes
0
replies
726
views
viewApply drops feature names; transfer names between lists
Coverage convert Coverage convert
7.7 years ago Chris Seidel ▴ 80
0
votes
5
replies
2.7k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Annotation graph Gviz Coverage Annotation graph Gviz
updated 7.7 years ago by ▴ 130 • written 7.7 years ago by ▴ 350
0
votes
0
replies
721
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Gviz Coverage Gviz
7.7 years ago Lance Parsons ▴ 130
1
vote
3
replies
2.7k
views
Blast analysis of two sequences in R
Coverage Coverage
updated 7.8 years ago by 25k • written 7.8 years ago by ▴ 100
0
votes
0
replies
3.1k
views
Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
7.8 years ago Dan Tenenbaum ★ 8.2k
0
votes
0
replies
994
views
easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
7.8 years ago Guest User ★ 12k
0
votes
3
replies
1.4k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 7.8 years ago by 15k • written 7.8 years ago by 11k
0
votes
0
replies
475
views
CIGAR-aware coverage
Coverage GenomicAlignments Coverage GenomicAlignments
7.9 years ago Hervé Pagès 15k
0
votes
8
replies
1.2k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 7.9 years ago by 11k • written 7.9 years ago by ▴ 30
0
votes
6
replies
1.6k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 7.9 years ago by 13k • written 7.9 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 8.0 years ago by ▴ 220 • written 8.0 years ago by ▴ 10
0
votes
2
replies
1.7k
views
Gviz - Visualize Reads - Color by Presence of Junction?
Coverage Gviz Coverage Gviz
updated 8.1 years ago by ▴ 710 • written 8.1 years ago by ▴ 120
0
votes
1
reply
980
views
ggbio: mirrored coverage plots for +/- strands
Coverage ggbio Coverage ggbio
updated 8.1 years ago by 11k • written 8.1 years ago by ★ 1.7k
0
votes
16
replies
2.9k
views
subset a RleList using GRanges object?
Coverage Cancer IRanges Coverage Cancer IRanges
updated 8.1 years ago by 15k • written 8.1 years ago by ▴ 740
50 results • Page 1 of 1
Recent ...
Replies
Comment: Trying to follow a gene set analyisis in R by Michael Love 35k
It looks like you only have a single sample.
Comment: Trying to follow a gene set analyisis in R by leonardorosas2001 • 0
I get the following > design = model.matrix(~ es$condition) > design (Intercept) es$conditiondex4 attr(,"assign") [1] 0 1 attr(,"co…
Comment: How to use subjunc for differential splicing analysis? by Yang Liao ▴ 280
Annotation to the *subjunc* aligner helps the aligner to better map the reads. The aligner generates BAM files, which contains mapped reads…
Answer: universalmotif, question about enrich_motifs function and number of hits returne by btremblay ▴ 30
Hi, After doing some digging I've isolated the issue to being related to the threshold calculation which you request with the `threshold…
Answer: DE analysis model matrix for paired samples by Michael Love 35k
Agree with swbarnes2. It just seems like the condition effect is very small. Also I'd double check the metadata. Sometimes samples are swap…
Votes
A: DNAcopy
Comment: Using DiffBind blacklists and greylists with results mapped to BDGP6
Answer: How to use subjunc for differential splicing analysis?
Answer: catchKallisto results are not counts
Answer: catchKallisto results are not counts
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