Showing : Coverage • reset
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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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1.5k
views
TEQC see all the reads with a given coverage
Coverage TEQC Coverage TEQC
13.5 years ago nac ▴ 280
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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
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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
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11
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5.0k
views
creating GRanges and reading BAM files
Coverage convert Coverage convert
updated 13.7 years ago by ▴ 80 • written 13.7 years ago by ▴ 70
0
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2
replies
1.6k
views
Coverage Question: GenomicRanges
Coverage convert Coverage convert
updated 13.7 years ago by ★ 11k • written 13.7 years ago by ▴ 250
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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
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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
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0
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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
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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
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3
replies
1.8k
views
Normalization in Coverage
Coverage Normalization Coverage Normalization
14.1 years ago rohan bareja ▴ 200
0
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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
14.1 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
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8
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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
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votes
4
replies
1.6k
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
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3
replies
3.0k
views
Any package to calculate NGS coverage and plot it?
Coverage Coverage
14.5 years ago Xiaohui Wu ▴ 280
0
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2
replies
1.3k
views
raw counts for edgeR
Coverage Coverage
updated 14.5 years ago by 21k • written 14.5 years ago by ★ 1.3k
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0
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1.2k
views
rtracklayer
Coverage Cancer Coverage Cancer
14.6 years ago Michael Lawrence ★ 11k
0
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0
replies
933
views
Extracting Data from SimpleRleViewsList
Coverage Coverage
14.6 years ago Lakshmanan Iyer ▴ 50
0
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0
replies
2.0k
views
Chip-Seq tag density plot
Coverage Cancer Coverage Cancer
14.6 years ago Eva Benito Garagorri ▴ 70
0
votes
0
replies
934
views
basic stats for methylC-seq type of methylation data
Coverage Coverage
14.8 years ago Steve Shen ▴ 330
0
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2
replies
1.1k
views
mapping coverage
Coverage Coverage
updated 14.8 years ago by 25k • written 14.8 years ago by ▴ 330
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2
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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 15.2 years ago by ▴ 100
0
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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
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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
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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
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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
2.3k
views
read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 16.2 years ago by 25k • written 16.2 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
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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
726
views
Comprehensive Healthcare List
Coverage Coverage
17.3 years ago pundit ▴ 10
0
votes
0
replies
934
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 19.3 years ago by ★ 13k • written 19.3 years ago by ▴ 50
152 results • Page 3 of 4
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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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