Showing : coverage • reset
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7
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2.0k
views
Amplicon and exon level read counts and GC content
Coverage Cancer Coverage Cancer
updated 13.5 years ago by 25k • written 13.5 years ago by ▴ 440
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0
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1.5k
views
TEQC see all the reads with a given coverage
Coverage TEQC Coverage TEQC
13.6 years ago nac ▴ 280
0
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1
reply
1.7k
views
FW: Overlay Gene Expression on SNP (copy number) data
SNP Coverage Network Cancer TranscriptDb IRanges RCytoscape ggbio Gviz SNP Coverage
updated 13.6 years ago by ★ 4.2k • written 13.6 years ago by ▴ 370
0
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1
reply
1.2k
views
seqbias : how to correct weight of mapped short reads?
Coverage IRanges seqbias Coverage IRanges seqbias
updated 13.6 years ago by 25k • written 13.6 years ago by ▴ 230
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1
reply
1.2k
views
RangedData Element Metadata
Coverage rtracklayer ASSIGN Coverage rtracklayer ASSIGN
updated 13.7 years ago by ★ 11k • written 13.7 years ago by ★ 1.6k
0
votes
11
replies
5.0k
views
creating GRanges and reading BAM files
Coverage convert Coverage convert
updated 13.8 years ago by ▴ 80 • written 13.8 years ago by ▴ 70
0
votes
2
replies
1.6k
views
Coverage Question: GenomicRanges
Coverage convert Coverage convert
updated 13.8 years ago by ★ 11k • written 13.8 years ago by ▴ 250
0
votes
4
replies
2.2k
views
htSeqTools errors
Coverage htSeqTools Coverage htSeqTools
updated 13.8 years ago by ★ 6.8k • written 13.8 years ago by ▴ 80
0
votes
2
replies
1.1k
views
Integer overflow when summing an 'integer' Rle
Coverage IRanges Coverage IRanges
updated 13.8 years ago by 16k • written 13.8 years ago by ★ 1.2k
0
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0
replies
1.5k
views
GenomeGraphs plots: polygon tracks for sequencing coverage data
Sequencing Coverage Visualization GenomeGraphs Sequencing Coverage Visualization
14.0 years ago Samuel Wuest ▴ 330
0
votes
3
replies
1.5k
views
Some more rtracklayer questions (re: WIG and .VSTEP files)
Coverage rtracklayer GenomicRanges Coverage rtracklayer GenomicRanges
updated 14.0 years ago by ★ 11k • written 14.0 years ago by ★ 4.2k
0
votes
7
replies
2.0k
views
export Views of Rle in rtracklayer
Coverage rtracklayer Coverage rtracklayer
updated 14.0 years ago by ★ 11k • written 14.0 years ago by ▴ 190
0
votes
3
replies
1.8k
views
Normalization in Coverage
Coverage Normalization Coverage Normalization
14.1 years ago rohan bareja ▴ 200
0
votes
0
replies
1.1k
views
Normalization in Coverage
Coverage Normalization Coverage Normalization
14.1 years ago rohan bareja ▴ 200
0
votes
2
replies
1.1k
views
Coverage of reads in 3'UTR
Coverage Coverage
14.1 years ago rohan bareja ▴ 200
0
votes
0
replies
1.2k
views
Using DESeq with ChIP-seq data - all or non-redundant reads?
Coverage Kidney DESeq Coverage Kidney DESeq
14.1 years ago Ivan Gregoretti ▴ 310
0
votes
17
replies
3.1k
views
Coverage by base
Coverage Coverage
14.2 years ago rohan bareja ▴ 200
0
votes
1
reply
1.2k
views
strand consistency with readAligned, coverage and transcriptsBy
Coverage Coverage
updated 14.2 years ago by ★ 13k • written 14.2 years ago by ▴ 220
0
votes
8
replies
3.9k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 14.3 years ago by 16k • written 14.3 years ago by ▴ 740
0
votes
4
replies
1.7k
views
IRanges: Request for a "step" argument in runsum
Coverage Annotation Cancer PROcess IRanges genomes Coverage Annotation Cancer PROcess
updated 14.4 years ago by 16k • written 14.4 years ago by ▴ 100
0
votes
3
replies
3.0k
views
Any package to calculate NGS coverage and plot it?
Coverage Coverage
14.5 years ago Xiaohui Wu ▴ 280
0
votes
2
replies
1.3k
views
raw counts for edgeR
Coverage Coverage
updated 14.6 years ago by 21k • written 14.6 years ago by ★ 1.3k
0
votes
0
replies
1.2k
views
rtracklayer
Coverage Cancer Coverage Cancer
14.6 years ago Michael Lawrence ★ 11k
0
votes
0
replies
935
views
Extracting Data from SimpleRleViewsList
Coverage Coverage
14.7 years ago Lakshmanan Iyer ▴ 50
0
votes
0
replies
2.0k
views
Chip-Seq tag density plot
Coverage Cancer Coverage Cancer
14.7 years ago Eva Benito Garagorri ▴ 70
0
votes
0
replies
941
views
basic stats for methylC-seq type of methylation data
Coverage Coverage
14.8 years ago Steve Shen ▴ 330
0
votes
2
replies
1.1k
views
mapping coverage
Coverage Coverage
updated 14.8 years ago by 25k • written 14.8 years ago by ▴ 330
0
votes
2
replies
1.1k
views
IRanges, GenomicRanges, GenomicFeatures?
Coverage Annotation TranscriptDb convert GenomicFeatures Coverage Annotation TranscriptDb
updated 15.1 years ago by ★ 13k • written 15.1 years ago by ▴ 60
0
votes
1
reply
1.3k
views
ShortRead qa() for BAM files?
Coverage Alignment ShortRead Coverage Alignment ShortRead
updated 15.2 years ago by 25k • written 15.2 years ago by ▴ 260
0
votes
2
replies
2.7k
views
Coverage vs GC bias - how to?
Coverage BSgenome BSgenome IRanges Coverage BSgenome BSgenome IRanges
updated 15.2 years ago by ▴ 590 • written 15.3 years ago by ▴ 100
0
votes
1
reply
1.4k
views
Involve tag count information in coverage function (IRanges, chipseq package)?
ChIPSeq Coverage chipseq ChIPSeq Coverage chipseq
15.3 years ago Xiaohui Wu ▴ 280
0
votes
3
replies
1.6k
views
gene2pathway retrain: which model is more complete?
Genetics Coverage biomaRt gene2pathway Genetics Coverage biomaRt gene2pathway
15.3 years ago Bogdan ▴ 50
0
votes
2
replies
1.2k
views
next-generation sequencing and embryogenisis
Sequencing SAGE Coverage Sequencing SAGE Coverage
updated 15.4 years ago by ▴ 330 • written 15.4 years ago by ▴ 20
0
votes
1
reply
1.5k
views
loop over IRanges spaces
Coverage convert rtracklayer ASSIGN Coverage convert rtracklayer ASSIGN
updated 15.6 years ago by ★ 11k • written 15.6 years ago by ▴ 60
0
votes
0
replies
1.1k
views
request: calculate coverage with weight on RangedData object
Coverage Cancer IRanges Coverage Cancer IRanges
15.7 years ago Janet Young ▴ 740
0
votes
1
reply
3.6k
views
color key - heatmap.2
Coverage Coverage
updated 15.7 years ago by 21k • written 15.7 years ago by ▴ 10
0
votes
2
replies
1.4k
views
IRanges:::coverage() speedup/enchancement
Coverage IRanges Coverage IRanges
updated 16.0 years ago by ▴ 290 • written 16.0 years ago by ★ 1.6k
0
votes
1
reply
1.1k
views
"islands" and number of reads in the island in package chipseq/ShortRead
ChIPSeq Coverage chipseq ChIPSeq Coverage chipseq
updated 16.0 years ago by ★ 6.5k • written 16.0 years ago by ▴ 40
0
votes
1
reply
1.1k
views
IRanges:::coverage() speedup/enchancement
Coverage IRanges Coverage IRanges
updated 16.0 years ago by ▴ 620 • written 16.0 years ago by ▴ 290
0
votes
5
replies
2.4k
views
read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 16.3 years ago by 25k • written 16.3 years ago by ▴ 40
0
votes
0
replies
5.9k
views
Reading GFF files into R and GenomeGraphs
Coverage Annotation Visualization convert GLAD GenomeGraphs rtracklayer IRanges Coverage
16.3 years ago Michael Dondrup ▴ 140
0
votes
2
replies
1.6k
views
interoperability between IRanges/ShortRead and rtracklayer
Coverage rtracklayer IRanges Coverage rtracklayer IRanges
updated 16.5 years ago by ★ 1.6k • written 16.5 years ago by ▴ 150
0
votes
0
replies
1.2k
views
Ensembl mart release 54: Useful information
Coverage zebrafish Coverage zebrafish
16.6 years ago Rhoda Kinsella ▴ 660
0
votes
1
reply
1.6k
views
A CGH platform question
SNP Genetics Coverage CGH affy SNP Genetics Coverage CGH affy
updated 17.0 years ago by ★ 2.4k • written 17.0 years ago by ▴ 70
0
votes
0
replies
728
views
Comprehensive Healthcare List
Coverage Coverage
17.3 years ago pundit ▴ 10
0
votes
0
replies
936
views
X:Map and 1.0 ST Gene Arrays, Introns
Coverage probe Coverage probe
17.4 years ago Thomas Hampton ▴ 750
0
votes
4
replies
1.5k
views
Opinions on array design, normalization, and linear modeling with LIMMA
Sequencing Coverage Normalization limma Sequencing Coverage Normalization limma
updated 18.1 years ago by ▴ 60 • written 18.1 years ago by ▴ 890
0
votes
3
replies
4.1k
views
from RefSeq to GO terms / gene symbol to geneID
Proteomics Coverage Annotation GO Proteomics Coverage Annotation GO
18.5 years ago • updated 18.4 years ago Simon Lin ▴ 270
0
votes
0
replies
1.1k
views
from RefSeq GI protein identifiers to GO terms
Proteomics Coverage GO Proteomics Coverage GO
18.5 years ago Lina Hultin-Rosenberg ▴ 80
0
votes
2
replies
2.0k
views
BH vs BY in p.adjust
Coverage limma safe Coverage limma safe
updated 19.4 years ago by ★ 13k • written 19.4 years ago by ▴ 50
152 results • Page 3 of 4
Recent ...
Replies
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…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
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
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