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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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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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
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Gviz - show plus and minus strand from a bam
Sequencing Coverage Gviz Sequencing Coverage Gviz
updated 12.0 years ago by ★ 1.6k • written 12.0 years ago by ▴ 510
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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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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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Computing the coverage on a bamfile with a huge amount of seqlevels
Coverage Coverage
updated 12.1 years ago by 16k • written 12.1 years ago by ▴ 360
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Bioconductor 2.13 is released
BiocViews aCGH SNP Transcription Sequencing miRNA Microarray Genetics Proteomics Coverage
12.1 years ago Dan Tenenbaum ★ 8.2k
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2
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1.6k
views
MEDIPS
Coverage MEDIPS Coverage MEDIPS
updated 12.1 years ago by ▴ 570 • written 12.1 years ago by ▴ 350
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1.1k
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about coverage profile comparison
Coverage Coverage
updated 12.2 years ago by ★ 13k • written 12.2 years ago by ▴ 500
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coverage() in IRanges gives >0 coverage when weight == 0
Coverage Coverage
updated 12.2 years ago by ▴ 290 • written 12.2 years ago by ▴ 40
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[devteam-bioc] Depth of Coverage and Base counts from BAM file
Coverage Cancer Rsamtools Coverage Cancer Rsamtools
12.2 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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Open position for an Experienced Researcher at Johannes Kepler University Linz, Austria
Coverage Coverage
12.3 years ago Secretary Institute of Bioinformatics ▴ 20
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8
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2.2k
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Filtering BAM files by start position for VariantTools
Coverage Cancer cycle VariantTools Coverage Cancer cycle VariantTools
updated 12.3 years ago by ▴ 250 • written 12.3 years ago by 25k
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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
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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
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[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Microarray Coverage Microarray Coverage
12.5 years ago Thomas Girke ★ 1.7k
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[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 12.5 years ago by ★ 13k • written 12.5 years ago by ▴ 330
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6
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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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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
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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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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
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3
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DESeq estimateDispersions
Coverage DESeq Coverage DESeq
updated 12.6 years ago by ★ 3.8k • written 12.6 years ago by ▴ 330
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5
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ensemblVEP: passing on coverage / frequency information
Coverage VariantTools ensemblVEP Coverage VariantTools ensemblVEP
updated 12.6 years ago by ★ 6.8k • written 12.6 years ago by ★ 13k
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Calculate Outer Positions of GappedAlignmentPairs
Coverage GenomicRanges Coverage GenomicRanges
updated 12.7 years ago by ★ 11k • written 12.7 years ago by ★ 1.6k
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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
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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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pileup coverage from BAM file
Coverage Coverage
12.8 years ago Chris Cabanski ▴ 30
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1
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2.5k
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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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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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[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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1.6k
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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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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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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
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Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
13.2 years ago Dan Tenenbaum ★ 8.2k
0
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1
reply
3.0k
views
Integer overflow when summing an 'integer' Rle
Coverage GO Cancer convert IRanges Coverage GO Cancer convert IRanges
updated 13.2 years ago by ★ 1.2k • written 13.2 years ago by ★ 6.8k
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using RUnit inspect() feature in package testing
Coverage Coverage
updated 13.3 years ago by ▴ 750 • written 13.3 years ago by ★ 1.1k
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3
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2.9k
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
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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
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912
views
Converting floating point RangedData to Rle
Coverage convert rtracklayer Coverage convert rtracklayer
13.4 years ago Marcin Imielinski ▴ 30
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6
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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
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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
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6
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1.7k
views
readGapppedAlignmentpairs questions
Coverage PROcess Coverage PROcess
updated 13.4 years ago by ★ 3.6k • written 13.4 years ago by ▴ 250
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0
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816
views
Coverage on GappedAlignment Pairs
Coverage PROcess Coverage PROcess
13.4 years ago Lakshmanan Iyer ▴ 50
0
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0
replies
805
views
Coverage on GappedAlignmentPairs
Coverage Coverage
13.4 years ago Lakshmanan Iyer ▴ 250
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1
reply
1.3k
views
TEQC package very slow
Coverage TEQC Coverage TEQC
13.5 years ago nac ▴ 280
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0
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1.6k
views
Working with GERP scores
Coverage Coverage
13.5 years ago Paul Leo ▴ 970
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0
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1.0k
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TEQC package isssue with chromosome format
Coverage Coverage
13.5 years ago nac ▴ 280
152 results • Page 2 of 4
Recent ...
Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
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
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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