Showing : coverage • reset
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ggbio: mirrored coverage plots for +/- strands
Coverage ggbio Coverage ggbio
updated 12.0 years ago by ★ 11k • written 12.0 years ago by ★ 1.7k
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16
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5.1k
views
subset a RleList using GRanges object?
Coverage Cancer IRanges Coverage Cancer IRanges
updated 12.0 years ago by 16k • written 12.0 years ago by ▴ 740
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1
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1.8k
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 12.0 years ago by ▴ 320 • written 12.0 years ago by 53k
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easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
12.0 years ago Nicolas Delhomme ▴ 320
5
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2
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3.6k
views
Gviz - show plus and minus strand from a bam
Sequencing Coverage Gviz Sequencing Coverage Gviz
updated 12.1 years ago by ★ 1.6k • written 12.1 years ago by ▴ 510
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1
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1.4k
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MEDIPS rms normalization by input
Coverage MEDIPS Coverage MEDIPS
updated 12.1 years ago by ▴ 570 • written 12.1 years ago by ★ 13k
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2
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7.3k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 12.1 years ago by ★ 11k • written 12.1 years ago by 16k
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10
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2.0k
views
Computing the coverage on a bamfile with a huge amount of seqlevels
Coverage Coverage
updated 12.2 years ago by 16k • written 12.2 years ago by ▴ 360
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4.7k
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Bioconductor 2.13 is released
BiocViews aCGH SNP Transcription Sequencing miRNA Microarray Genetics Proteomics Coverage
12.2 years ago Dan Tenenbaum ★ 8.2k
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2
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1.6k
views
MEDIPS
Coverage MEDIPS Coverage MEDIPS
updated 12.2 years ago by ▴ 570 • written 12.2 years ago by ▴ 350
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1
reply
1.1k
views
about coverage profile comparison
Coverage Coverage
updated 12.3 years ago by ★ 13k • written 12.3 years ago by ▴ 500
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1
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1.1k
views
coverage() in IRanges gives >0 coverage when weight == 0
Coverage Coverage
updated 12.3 years ago by ▴ 290 • written 12.3 years ago by ▴ 40
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1
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1.0k
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[devteam-bioc] Depth of Coverage and Base counts from BAM file
Coverage Cancer Rsamtools Coverage Cancer Rsamtools
12.3 years ago Hervé Pagès 16k
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Connectionists: Open position for an Experienced Researcher at Johannes Kepler University Linz, Austria
Coverage PROcess Coverage PROcess
12.3 years ago Secretary Institute of Bioinformatics ▴ 20
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0
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1.2k
views
Open position for an Experienced Researcher at Johannes Kepler University Linz, Austria
Coverage Coverage
12.3 years ago Secretary Institute of Bioinformatics ▴ 20
0
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8
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2.2k
views
Filtering BAM files by start position for VariantTools
Coverage Cancer cycle VariantTools Coverage Cancer cycle VariantTools
updated 12.4 years ago by ▴ 250 • written 12.4 years ago by 25k
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0
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929
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MEDIPS differential coverage
Coverage MEDIPS Coverage MEDIPS
12.5 years ago Sara Castelletti ▴ 40
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4
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2.1k
views
Rsamtools: Realloc integer overflow?
Coverage Coverage
updated 12.5 years ago by 25k • written 12.5 years ago by ★ 11k
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10
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1.9k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Microarray Coverage Microarray Coverage
12.6 years ago Thomas Girke ★ 1.7k
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17
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3.8k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 12.6 years ago by ★ 13k • written 12.6 years ago by ▴ 330
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6
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2.1k
views
coverage on very large ReadGappedAlignmentsObject
Coverage genomes Coverage genomes
updated 12.6 years ago by 25k • written 12.6 years ago by ▴ 360
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3
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1.5k
views
Deleting object rows while looping - II
Coverage Alignment Cancer PROcess Coverage Alignment Cancer PROcess
updated 12.6 years ago by ★ 13k • written 12.6 years ago by 16k
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2
replies
2.1k
views
cn.mops: copy number for low-coverage bam files?
Sequencing Coverage cn.mops Sequencing Coverage cn.mops
updated 12.6 years ago by ▴ 540 • written 12.6 years ago by ▴ 750
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3
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1.8k
views
Deleting object rows while looping - II
Coverage Alignment PROcess Coverage Alignment PROcess
updated 12.6 years ago by 25k • written 12.6 years ago by ▴ 90
0
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3
replies
4.4k
views
DESeq estimateDispersions
Coverage DESeq Coverage DESeq
updated 12.7 years ago by ★ 3.8k • written 12.7 years ago by ▴ 330
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5
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2.6k
views
ensemblVEP: passing on coverage / frequency information
Coverage VariantTools ensemblVEP Coverage VariantTools ensemblVEP
updated 12.7 years ago by ★ 6.8k • written 12.7 years ago by ★ 13k
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10
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2.2k
views
Calculate Outer Positions of GappedAlignmentPairs
Coverage GenomicRanges Coverage GenomicRanges
updated 12.7 years ago by ★ 11k • written 12.7 years ago by ★ 1.6k
1
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0
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2.2k
views
pileup coverage from BAM file
Coverage Cancer IRanges GenomicRanges Coverage Cancer IRanges GenomicRanges
12.8 years ago Martin Morgan 25k
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5
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2.2k
views
Visualization of alignments with mismatch bases
SNP Coverage Alignment Visualization ggbio SNP Coverage Alignment Visualization ggbio
updated 12.8 years ago by ▴ 420 • written 12.8 years ago by ★ 11k
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0
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1.7k
views
pileup coverage from BAM file
Coverage Coverage
12.8 years ago Chris Cabanski ▴ 30
0
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1
reply
2.5k
views
Bioconductor Digest, Vol 120, Issue 12
Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy
12.8 years ago Matthew Thornton ▴ 390
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3
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1.5k
views
speed of runmed on SimpleRleList
Coverage Cancer Coverage Cancer
updated 12.8 years ago by 16k • written 12.8 years ago by ▴ 740
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2
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1.8k
views
[devteam-bioc] Can you give me a sample to calculate the Read Depth with Rsamtools?
Coverage Cancer Rsamtools Coverage Cancer Rsamtools
updated 12.9 years ago by ▴ 10 • written 12.9 years ago by 25k
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1
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1.6k
views
Detection copy number variations with cn.MOPS package
Coverage cn.mops Coverage cn.mops
updated 13.0 years ago by ▴ 540 • written 13.0 years ago by ▴ 50
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1
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1.3k
views
IRanges install error with parallel/mcmapply
Coverage IRanges Coverage IRanges
updated 13.0 years ago by ★ 8.2k • written 13.0 years ago by ▴ 10
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1
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2.3k
views
compilation failed for package \'IRanges\' @str_utils.c(152) identifier \"timezone\" is undefined
Coverage IRanges Coverage IRanges
updated 13.1 years ago by ★ 8.2k • written 13.1 years ago by ★ 13k
0
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0
replies
3.6k
views
Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
13.2 years ago Dan Tenenbaum ★ 8.2k
0
votes
1
reply
3.0k
views
Integer overflow when summing an 'integer' Rle
Coverage GO Cancer convert IRanges Coverage GO Cancer convert IRanges
updated 13.3 years ago by ★ 1.2k • written 13.3 years ago by ★ 6.8k
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2
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1.4k
views
using RUnit inspect() feature in package testing
Coverage Coverage
updated 13.3 years ago by ▴ 750 • written 13.3 years ago by ★ 1.1k
0
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3
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3.0k
views
Coverage of reads per base position from BAM files
Coverage GO Coverage GO
updated 13.4 years ago by 25k • written 13.4 years ago by ★ 13k
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2
replies
2.3k
views
Wig files?
Coverage Coverage
updated 13.4 years ago by ★ 11k • written 13.4 years ago by ▴ 230
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0
replies
919
views
Converting floating point RangedData to Rle
Coverage convert rtracklayer Coverage convert rtracklayer
13.4 years ago Marcin Imielinski ▴ 30
0
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6
replies
2.0k
views
IRanges coverage integer limit?
Coverage IRanges Coverage IRanges
updated 13.4 years ago by 16k • written 13.4 years ago by ★ 1.2k
0
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1
reply
1.1k
views
IRanges: the width argument of the coverage function
Coverage Coverage
updated 13.4 years ago by 16k • written 13.4 years ago by ★ 1.2k
0
votes
6
replies
1.7k
views
readGapppedAlignmentpairs questions
Coverage PROcess Coverage PROcess
updated 13.5 years ago by ★ 3.6k • written 13.5 years ago by ▴ 250
0
votes
0
replies
818
views
Coverage on GappedAlignment Pairs
Coverage PROcess Coverage PROcess
13.5 years ago Lakshmanan Iyer ▴ 50
0
votes
0
replies
810
views
Coverage on GappedAlignmentPairs
Coverage Coverage
13.5 years ago Lakshmanan Iyer ▴ 250
0
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1
reply
1.4k
views
TEQC package very slow
Coverage TEQC Coverage TEQC
13.5 years ago nac ▴ 280
0
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0
replies
1.7k
views
Working with GERP scores
Coverage Coverage
13.5 years ago Paul Leo ▴ 970
0
votes
0
replies
1.0k
views
TEQC package isssue with chromosome format
Coverage Coverage
13.5 years ago nac ▴ 280
152 results • Page 2 of 4
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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