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 11.1 years ago by ★ 11k • written 11.1 years ago by 16k
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Reading GFF files into R and GenomeGraphs
Coverage Annotation Visualization convert GLAD GenomeGraphs rtracklayer IRanges Coverage
15.3 years ago Michael Dondrup ▴ 140
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2
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.7 years ago by ▴ 20 • written 2.7 years ago by • 0
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11
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4.4k
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creating GRanges and reading BAM files
Coverage convert Coverage convert
updated 12.7 years ago by ▴ 80 • written 12.8 years ago by ▴ 70
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16
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4.4k
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subset a RleList using GRanges object?
Coverage Cancer IRanges Coverage Cancer IRanges
updated 11.0 years ago by 16k • written 11.0 years ago by ▴ 740
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Bioconductor 2.13 is released
BiocViews aCGH SNP Transcription Sequencing miRNA Microarray Genetics Proteomics Coverage
11.1 years ago Dan Tenenbaum ★ 8.2k
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4.3k
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Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
10.6 years ago Dan Tenenbaum ★ 8.2k
1
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3
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Blast analysis of two sequences in R
Coverage Coverage
updated 10.6 years ago by 25k • written 10.6 years ago by ▴ 100
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3
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4.1k
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DESeq estimateDispersions
Coverage DESeq Coverage DESeq
updated 11.6 years ago by ★ 3.8k • written 11.6 years ago by ▴ 330
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Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 9.4 years ago by • 0 • written 11.7 years ago by ★ 8.2k
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5
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3.8k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Annotation graph Gviz Coverage Annotation graph Gviz
updated 10.6 years ago by ▴ 130 • written 10.6 years ago by ▴ 350
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3
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3.6k
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from RefSeq to GO terms / gene symbol to geneID
Proteomics Coverage Annotation GO Proteomics Coverage Annotation GO
17.5 years ago • updated 17.4 years ago Simon Lin ▴ 270
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8
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3.5k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 13.3 years ago by 16k • written 13.3 years ago by ▴ 740
5
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2
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3.3k
views
Gviz - show plus and minus strand from a bam
Sequencing Coverage Gviz Sequencing Coverage Gviz
updated 11.1 years ago by ★ 1.6k • written 11.1 years ago by ▴ 510
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1
reply
3.3k
views
color key - heatmap.2
Coverage Coverage
updated 14.7 years ago by 21k • written 14.7 years ago by ▴ 10
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1
reply
3.3k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
10.6 years ago florian.hahne@novartis.com ★ 1.6k
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views
Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
12.2 years ago Dan Tenenbaum ★ 8.2k
6
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0
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3.1k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma
18.4 years ago • updated 8.9 years ago Gordon Smyth 52k
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17
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3.0k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ▴ 330
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6
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3.0k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 30
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4
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3.0k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 13 months ago by • 0 • written 10.2 years ago by ★ 13k
1
vote
2
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2.9k
views
"Normalising" GRanges coverage object
Coverage GO Gviz Coverage GO Gviz
updated 10.3 years ago by ★ 7.9k • written 10.3 years ago by ▴ 350
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6
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2.9k
views
Displaying very deep coverage in Gviz
Coverage Gviz Coverage Gviz
updated 10.6 years ago by ★ 1.6k • written 10.6 years ago by ▴ 130
6
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3
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2.9k
views
how does coverage() works
biostrings coverage rle iranges
8.5 years ago likeeatingpizza ▴ 10
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1
reply
2.7k
views
Integer overflow when summing an 'integer' Rle
Coverage GO Cancer convert IRanges Coverage GO Cancer convert IRanges
updated 12.3 years ago by ★ 1.2k • written 12.3 years ago by ★ 6.8k
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3
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2.7k
views
Any package to calculate NGS coverage and plot it?
Coverage Coverage
13.5 years ago Xiaohui Wu ▴ 280
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3
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2.7k
views
Coverage of reads per base position from BAM files
Coverage GO Coverage GO
updated 12.4 years ago by 25k • written 12.4 years ago by ★ 13k
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2
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2.6k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma Coverage limma
updated 8.9 years ago by 52k • written 18.4 years ago by ▴ 50
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6
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2.6k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 10.8 years ago by ★ 13k • written 10.8 years ago by ▴ 170
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17
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2.4k
views
Coverage by base
Coverage Coverage
13.2 years ago • updated 13.1 years ago rohan bareja ▴ 200
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2
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2.4k
views
Coverage vs GC bias - how to?
Coverage BSgenome BSgenome IRanges Coverage BSgenome BSgenome IRanges
updated 14.2 years ago by ▴ 590 • written 14.2 years ago by ▴ 100
1
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3
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2.4k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 10.7 years ago by 16k • written 10.7 years ago by ★ 11k
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1
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2.4k
views
Bioconductor Digest, Vol 120, Issue 12
Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy
11.8 years ago Matthew Thornton ▴ 380
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2
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2.3k
views
Gviz - Visualize Reads - Color by Presence of Junction?
Coverage Gviz Coverage Gviz
updated 11.0 years ago by ▴ 750 • written 11.0 years ago by ▴ 120
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5
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SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
9.6 years ago maria.maqueda • 0
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5
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2.2k
views
ensemblVEP: passing on coverage / frequency information
Coverage VariantTools ensemblVEP Coverage VariantTools ensemblVEP
updated 11.7 years ago by ★ 6.8k • written 11.7 years ago by ★ 13k
0
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1
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2.2k
views
compilation failed for package \'IRanges\' @str_utils.c(152) identifier \"timezone\" is undefined
Coverage IRanges Coverage IRanges
updated 12.1 years ago by ★ 8.2k • written 12.1 years ago by ★ 13k
2
votes
5
replies
2.2k
views
GOseq: count bias correction variations?
Coverage goseq
updated 7.6 years ago by 52k • written 10.4 years ago by ▴ 40
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0
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2.1k
views
problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name
Coverage Annotation rtracklayer Coverage Annotation rtracklayer
10.5 years ago Marco Blanchette ▴ 220
1
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2
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2.1k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 9.4 years ago by 25k • written 9.4 years ago by ▴ 90
3
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2
replies
2.1k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 6.8 years ago by 16k • written 6.8 years ago by ▴ 10
0
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1
reply
2.1k
views
Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
wiggleplotr bigwig coverage ngs
updated 7.2 years ago by ▴ 30 • written 7.2 years ago by • 0
0
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5
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2.1k
views
read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 15.3 years ago by 25k • written 15.3 years ago by ▴ 40
0
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2
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2.0k
views
Wig files?
Coverage Coverage
updated 12.4 years ago by ★ 11k • written 12.4 years ago by ▴ 230
0
votes
4
replies
2.0k
views
htSeqTools errors
Coverage htSeqTools Coverage htSeqTools
updated 12.8 years ago by ★ 6.8k • written 12.8 years ago by ▴ 80
1
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0
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2.0k
views
pileup coverage from BAM file
Coverage Cancer IRanges GenomicRanges Coverage Cancer IRanges GenomicRanges
11.8 years ago Martin Morgan 25k
0
votes
8
replies
2.0k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 10.8 years ago by ★ 11k • written 10.8 years ago by ▴ 30
5
votes
3
replies
1.9k
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 9.6 years ago by 16k • written 9.6 years ago by ▴ 10
0
votes
2
replies
1.9k
views
cn.mops: copy number for low-coverage bam files?
Sequencing Coverage cn.mops Sequencing Coverage cn.mops
updated 11.6 years ago by ▴ 540 • written 11.6 years ago by ▴ 750
0
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4
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1.9k
views
Rsamtools: Realloc integer overflow?
Coverage Coverage
updated 11.5 years ago by 25k • written 11.5 years ago by ★ 11k
50 results • Page 1 of 1
Recent ...
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Comment: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You can examine the structure of a `DelayedMatrix` by calling the `showtree()` function. For example: ``` library(scRNAseq) X <- fetchData…
Comment: lfcShrink and alpha value by cropero • 0
Thank you so much! Would that be equivalent to perform `res <- results(dds, contrast = c("conditions", "wild_type_114_2_no_carbon", "wild_t…
Comment: pathview - multiple states by Philippine • 0
Thank you! Here a subset of genes that really works with "ame04145". data <- data.frame( EntrezID = c(100577548, 100577764, 406…
Comment: pathview - multiple states by Guido Hooiveld ★ 4.1k
A quick comment after I copied/pasted your code: when using `geneList1` in the 3rd code chunk I do **not** get a nice plot... I rather got …
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Adam • 0
Hi Aaron, Thanks a lot for your help! As you mentioned, I checked my data and it is "DelayedMatrix". I don't know the detailed differe…
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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