Showing : Coverage • reset
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Coverage by base
Coverage Coverage
12.6 years ago • updated 12.5 years ago rohan bareja ▴ 200
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10
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1.3k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Microarray Coverage Microarray Coverage
10.9 years ago Thomas Girke ★ 1.7k
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5
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1.9k
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read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 14.6 years ago by 25k • written 14.7 years ago by ▴ 40
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3
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1.2k
views
gene2pathway retrain: which model is more complete?
Genetics Coverage biomaRt gene2pathway Genetics Coverage biomaRt gene2pathway
13.7 years ago Bogdan ▴ 50
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6
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2.6k
views
Displaying very deep coverage in Gviz
Coverage Gviz Coverage Gviz
updated 9.9 years ago by ★ 1.6k • written 9.9 years ago by ▴ 130
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16
replies
4.1k
views
subset a RleList using GRanges object?
Coverage Cancer IRanges Coverage Cancer IRanges
updated 10.4 years ago by 16k • written 10.4 years ago by ▴ 740
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3
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2.5k
views
Any package to calculate NGS coverage and plot it?
Coverage Coverage
12.9 years ago Xiaohui Wu ▴ 280
0
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3
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3.3k
views
from RefSeq to GO terms / gene symbol to geneID
Proteomics Coverage Annotation GO Proteomics Coverage Annotation GO
16.9 years ago • updated 16.8 years ago Simon Lin ▴ 270
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2
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3.8k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 8.8 years ago by • 0 • written 11.1 years ago by ★ 8.2k
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3
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1.4k
views
Normalization in Coverage
Coverage Normalization Coverage Normalization
12.5 years ago rohan bareja ▴ 200
0
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2
replies
858
views
Coverage of reads in 3'UTR
Coverage Coverage
12.5 years ago rohan bareja ▴ 200
0
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2
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1.6k
views
mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 9.9 years ago by ▴ 240 • written 9.9 years ago by ▴ 10
1
vote
3
replies
2.2k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 10.1 years ago by 16k • written 10.1 years ago by ★ 11k
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2
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910
views
next-generation sequencing and embryogenisis
Sequencing SAGE Coverage Sequencing SAGE Coverage
updated 13.8 years ago by ▴ 330 • written 13.8 years ago by ▴ 20
0
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3
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1.1k
views
Deleting object rows while looping - II
Coverage Alignment Cancer PROcess Coverage Alignment Cancer PROcess
updated 11.0 years ago by ★ 13k • written 11.0 years ago by 16k
1
vote
2
replies
1.5k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 4.5 years ago by ★ 11k • written 7.1 years ago by ▴ 10
0
votes
8
replies
1.8k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 30
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5
replies
2.0k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
9.0 years ago maria.maqueda • 0
0
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2
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1.0k
views
using RUnit inspect() feature in package testing
Coverage Coverage
updated 11.7 years ago by ▴ 750 • written 11.7 years ago by ★ 1.1k
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4
replies
2.6k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 6 months ago by • 0 • written 9.6 years ago by ★ 13k
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8
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3.4k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 12.7 years ago by 16k • written 12.7 years ago by ▴ 740
0
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2
replies
3.6k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.1 years ago by ▴ 20 • written 2.1 years ago by • 0
0
votes
2
replies
6.3k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 10.5 years ago by ★ 11k • written 10.5 years ago by 16k
0
votes
7
replies
1.4k
views
export Views of Rle in rtracklayer
Coverage rtracklayer Coverage rtracklayer
updated 12.4 years ago by ★ 11k • written 12.4 years ago by ▴ 190
6
votes
3
replies
2.4k
views
how does coverage() works
biostrings coverage rle iranges
7.9 years ago likeeatingpizza ▴ 10
0
votes
17
replies
2.6k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 10.9 years ago by ★ 13k • written 10.9 years ago by ▴ 330
0
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3
replies
3.8k
views
DESeq estimateDispersions
Coverage DESeq Coverage DESeq
updated 11.0 years ago by ★ 3.7k • written 11.0 years ago by ▴ 330
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3
replies
2.4k
views
Coverage of reads per base position from BAM files
Coverage GO Coverage GO
updated 11.8 years ago by 25k • written 11.8 years ago by ★ 13k
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2
replies
2.3k
views
Coverage vs GC bias - how to?
Coverage BSgenome BSgenome IRanges Coverage BSgenome BSgenome IRanges
updated 13.6 years ago by ▴ 590 • written 13.6 years ago by ▴ 100
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2
replies
2.4k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma Coverage limma
updated 8.3 years ago by 50k • written 17.7 years ago by ▴ 50
0
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11
replies
4.0k
views
creating GRanges and reading BAM files
Coverage convert Coverage convert
updated 12.1 years ago by ▴ 80 • written 12.1 years ago by ▴ 70
0
votes
3
replies
1.5k
views
Deleting object rows while looping - II
Coverage Alignment PROcess Coverage Alignment PROcess
updated 11.0 years ago by 25k • written 11.0 years ago by ▴ 90
0
votes
6
replies
1.1k
views
readGapppedAlignmentpairs questions
Coverage PROcess Coverage PROcess
updated 11.8 years ago by ★ 3.6k • written 11.8 years ago by ▴ 250
0
votes
2
replies
1.5k
views
[devteam-bioc] Can you give me a sample to calculate the Read Depth with Rsamtools?
Coverage Cancer Rsamtools Coverage Cancer Rsamtools
updated 11.3 years ago by ▴ 10 • written 11.3 years ago by 25k
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6
replies
2.3k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 10.2 years ago by ★ 13k • written 10.2 years ago by ▴ 170
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1
reply
1.2k
views
loop over IRanges spaces
Coverage convert rtracklayer ASSIGN Coverage convert rtracklayer ASSIGN
updated 14.0 years ago by ★ 11k • written 14.0 years ago by ▴ 60
0
votes
1
reply
885
views
tiling/SNP microarrays
SNP Coverage tilingArray SNP Coverage tilingArray
updated 17.8 years ago by 21k • written 17.8 years ago by ▴ 10
0
votes
1
reply
3.1k
views
color key - heatmap.2
Coverage Coverage
updated 14.1 years ago by 21k • written 14.1 years ago by ▴ 10
0
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2
replies
1.7k
views
Wig files?
Coverage Coverage
updated 11.8 years ago by ★ 11k • written 11.8 years ago by ▴ 230
0
votes
1
reply
832
views
"islands" and number of reads in the island in package chipseq/ShortRead
ChIPSeq Coverage chipseq ChIPSeq Coverage chipseq
updated 14.4 years ago by ★ 6.5k • written 14.4 years ago by ▴ 40
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2
replies
1.1k
views
IRanges:::coverage() speedup/enchancement
Coverage IRanges Coverage IRanges
updated 14.4 years ago by ▴ 290 • written 14.4 years ago by ★ 1.6k
0
votes
4
replies
1.1k
views
Opinions on array design, normalization, and linear modeling with LIMMA
Sequencing Coverage Normalization limma Sequencing Coverage Normalization limma
updated 16.5 years ago by ▴ 60 • written 16.5 years ago by ▴ 890
0
votes
1
reply
836
views
IRanges:::coverage() speedup/enchancement
Coverage IRanges Coverage IRanges
updated 14.4 years ago by ▴ 620 • written 14.4 years ago by ▴ 290
0
votes
1
reply
1.3k
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 10.4 years ago by ▴ 320 • written 10.4 years ago by 50k
0
votes
1
reply
810
views
IRanges: the width argument of the coverage function
Coverage Coverage
updated 11.8 years ago by 16k • written 11.8 years ago by ★ 1.2k
0
votes
6
replies
1.5k
views
IRanges coverage integer limit?
Coverage IRanges Coverage IRanges
updated 11.8 years ago by 16k • written 11.8 years ago by ★ 1.2k
0
votes
1
reply
915
views
seqbias : how to correct weight of mapped short reads?
Coverage IRanges seqbias Coverage IRanges seqbias
updated 12.0 years ago by 25k • written 12.0 years ago by ▴ 230
0
votes
1
reply
898
views
strand consistency with readAligned, coverage and transcriptsBy
Coverage Coverage
updated 12.6 years ago by ★ 13k • written 12.6 years ago by ▴ 220
0
votes
2
replies
1.2k
views
interoperability between IRanges/ShortRead and rtracklayer
Coverage rtracklayer IRanges Coverage rtracklayer IRanges
updated 14.9 years ago by ★ 1.6k • written 14.9 years ago by ▴ 150
0
votes
7
replies
1.6k
views
Amplicon and exon level read counts and GC content
Coverage Cancer Coverage Cancer
updated 11.9 years ago by 25k • written 11.9 years ago by ▴ 440
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Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp by clacarion • 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Answer: List of Deprecated Packages for Bioc3.19 by shepherl 3.8k
singleCellTK has been fixed and will remain in Bioconductor
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
Yes, I'm working only with genes from terpenoids pathway (14 genes), so I can't use enrichGO? Can you recommend a package or something like…
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
Your awnser at Cannabis orgDb solve my problems using enrichGO by far. I'm underdegree biotechnology student, and I learning bioinformatic…
Votes
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
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