Showing : Coverage • reset
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how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 10.5 years ago by ★ 11k • written 10.5 years ago by 16k
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Reading GFF files into R and GenomeGraphs
Coverage Annotation Visualization convert GLAD GenomeGraphs rtracklayer IRanges Coverage
14.7 years ago Michael Dondrup ▴ 140
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16
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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
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4.1k
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
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0
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4.0k
views
Bioconductor 2.13 is released
BiocViews aCGH SNP Transcription Sequencing miRNA Microarray Genetics Proteomics Coverage
10.5 years ago Dan Tenenbaum ★ 8.2k
0
votes
11
replies
4.0k
views
creating GRanges and reading BAM files
Coverage convert Coverage convert
updated 12.1 years ago by ▴ 80 • written 12.1 years ago by ▴ 70
1
vote
3
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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
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votes
2
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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
0
votes
3
replies
3.8k
views
DESeq estimateDispersions
Coverage DESeq Coverage DESeq
updated 11.0 years ago by ★ 3.7k • written 11.0 years ago by ▴ 330
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2
replies
3.7k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.1 years ago by ▴ 20 • written 2.1 years ago by • 0
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
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8
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3.4k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 12.7 years ago by 16k • written 12.7 years ago by ▴ 740
0
votes
3
replies
3.3k
views
from RefSeq to GO terms / gene symbol to geneID
Proteomics Coverage Annotation GO Proteomics Coverage Annotation GO
16.9 years ago • updated 16.8 years ago Simon Lin ▴ 270
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
1
reply
3.1k
views
color key - heatmap.2
Coverage Coverage
updated 14.1 years ago by 21k • written 14.1 years ago by ▴ 10
0
votes
0
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3.1k
views
Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
11.6 years ago Dan Tenenbaum ★ 8.2k
5
votes
2
replies
3.1k
views
Gviz - show plus and minus strand from a bam
Sequencing Coverage Gviz Sequencing Coverage Gviz
updated 10.5 years ago by ★ 1.6k • written 10.5 years ago by ▴ 490
6
votes
0
replies
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
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
17
replies
2.7k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 11.0 years ago by ★ 13k • written 11.0 years ago by ▴ 330
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
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
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
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votes
3
replies
2.5k
views
Any package to calculate NGS coverage and plot it?
Coverage Coverage
12.9 years ago Xiaohui Wu ▴ 280
0
votes
1
reply
2.5k
views
Integer overflow when summing an 'integer' Rle
Coverage GO Cancer convert IRanges Coverage GO Cancer convert IRanges
updated 11.6 years ago by ★ 1.2k • written 11.6 years ago by ★ 6.8k
0
votes
3
replies
2.5k
views
Coverage of reads per base position from BAM files
Coverage GO Coverage GO
updated 11.8 years ago by 25k • written 11.8 years ago by ★ 13k
0
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2
replies
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
6
votes
3
replies
2.4k
views
how does coverage() works
biostrings coverage rle iranges
7.9 years ago likeeatingpizza ▴ 10
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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2
replies
2.3k
views
Coverage vs GC bias - how to?
Coverage BSgenome BSgenome IRanges Coverage BSgenome BSgenome IRanges
updated 13.6 years ago by ▴ 590 • written 13.6 years ago by ▴ 100
0
votes
1
reply
2.2k
views
Bioconductor Digest, Vol 120, Issue 12
Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy
11.2 years ago Matthew Thornton ▴ 350
0
votes
17
replies
2.2k
views
Coverage by base
Coverage Coverage
12.6 years ago • updated 12.5 years ago rohan bareja ▴ 200
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
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
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1
reply
2.0k
views
compilation failed for package \'IRanges\' @str_utils.c(152) identifier \"timezone\" is undefined
Coverage IRanges Coverage IRanges
updated 11.5 years ago by ★ 8.2k • written 11.5 years ago by ★ 13k
0
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0
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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
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
0
votes
5
replies
2.0k
views
ensemblVEP: passing on coverage / frequency information
Coverage VariantTools ensemblVEP Coverage VariantTools ensemblVEP
updated 11.1 years ago by ★ 6.8k • written 11.1 years ago by ★ 13k
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
2
votes
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
0
votes
5
replies
1.9k
views
read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 14.7 years ago by 25k • written 14.7 years ago by ▴ 40
1
vote
0
replies
1.9k
views
pileup coverage from BAM file
Coverage Cancer IRanges GenomicRanges Coverage Cancer IRanges GenomicRanges
11.2 years ago Martin Morgan 25k
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
4
replies
1.8k
views
Rsamtools: Realloc integer overflow?
Coverage Coverage
updated 10.9 years ago by 25k • written 10.9 years ago by ★ 11k
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
4
replies
1.8k
views
htSeqTools errors
Coverage htSeqTools Coverage htSeqTools
updated 12.2 years ago by ★ 6.8k • written 12.2 years ago by ▴ 80
5
votes
3
replies
1.8k
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
0
votes
2
replies
1.7k
views
Wig files?
Coverage Coverage
updated 11.8 years ago by ★ 11k • written 11.8 years ago by ▴ 230
0
votes
2
replies
1.7k
views
cn.mops: copy number for low-coverage bam files?
Sequencing Coverage cn.mops Sequencing Coverage cn.mops
updated 11.0 years ago by ▴ 540 • written 11.0 years ago by ▴ 750
0
votes
0
replies
1.7k
views
Chip-Seq tag density plot
Coverage Cancer Coverage Cancer
13.1 years ago Eva Benito Garagorri ▴ 70
50 results • Page 1 of 1
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 30
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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