Showing : Coverage • reset
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.1 years ago by ▴ 20 • written 2.1 years ago by • 0
3
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4
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1.0k
views
Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
2.6 years ago Rui ▴ 10
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4
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1.2k
views
AlignmentsTrack empty plot
Coverage RNASeq plot Gviz
updated 15 months ago by 65k • written 2.7 years ago by • 0
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0
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724
views
Can you compute summary stats of coverage directly when importing using rtracklayer?
Coverage rtracklayer
3.5 years ago David • 0
0
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1
reply
921
views
How to convert bedgraph.sorted or wig files to coverage files
bedgraph .cov wig biseq coverage
3.8 years ago akhaira • 0
1
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2
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1.5k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 4.6 years ago by ★ 11k • written 7.1 years ago by ▴ 10
0
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3
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1.2k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
5.5 years ago faramer86 • 0
0
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1
reply
985
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
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2
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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
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0
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1.3k
views
DSS CpG coverage threshold
DSS WGBS coverage
6.6 years ago floriandeckert ▴ 30
0
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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
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1
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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
2
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5
replies
1.9k
views
GOseq: count bias correction variations?
Coverage goseq
updated 7.0 years ago by 50k • written 9.8 years ago by ▴ 40
1
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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
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2
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1.6k
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 7.3 years ago by • 0 • written 7.3 years ago by ▴ 40
0
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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
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0
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1.3k
views
RNA-Seq metagene coverage
coverage
7.8 years ago Jake ▴ 90
0
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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
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3
replies
2.4k
views
how does coverage() works
biostrings coverage rle iranges
7.9 years ago likeeatingpizza ▴ 10
2
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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
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2
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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
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3
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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
6
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0
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2.8k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma
17.8 years ago • updated 8.3 years ago Gordon Smyth 50k
0
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2
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2.4k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma Coverage limma
updated 8.3 years ago by 50k • written 17.8 years ago by ▴ 50
0
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2
replies
3.8k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 8.8 years ago by • 0 • written 11.1 years ago by ★ 8.2k
1
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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
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5
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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
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3
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1.8k
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 10
2
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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
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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
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0
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1.3k
views
ggbio plot coverage adjusted for library size
Coverage Normalization Coverage Normalization
9.7 years ago Tengfei Yin ▴ 490
1
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2
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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
0
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0
replies
1.2k
views
ggbio plot coverage adjusted for library size
Coverage Coverage
9.8 years ago James W. MacDonald 65k
0
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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
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1
reply
3.2k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
10.0 years ago florian.hahne@novartis.com ★ 1.6k
0
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2
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1.6k
views
mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 10.0 years ago by ▴ 240 • written 10.0 years ago by ▴ 10
0
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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
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0
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1.2k
views
viewApply drops feature names; transfer names between lists
Coverage convert Coverage convert
10.0 years ago Chris Seidel ▴ 80
0
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5
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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
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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
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0
replies
4.1k
views
Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
10.1 years ago Dan Tenenbaum ★ 8.2k
0
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0
replies
1.5k
views
easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
10.1 years ago Guest User ★ 13k
1
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3
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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
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0
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785
views
CIGAR-aware coverage
Coverage GenomicAlignments Coverage GenomicAlignments
10.2 years ago Hervé Pagès 16k
0
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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
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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
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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
50 results • Page 1 of 1
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Answer: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by James W. MacDonald 65k
You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…
Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
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SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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