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 10.0 years ago by ★ 1.6k • written 10.0 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
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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
votes
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
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3
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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
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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
votes
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
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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
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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
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3
replies
2.4k
views
how does coverage() works
biostrings coverage rle iranges
7.9 years ago likeeatingpizza ▴ 10
0
votes
17
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2.7k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 11.0 years ago by ★ 13k • written 11.0 years ago by ▴ 330
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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
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2.5k
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
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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 17.8 years ago by ▴ 50
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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
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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
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2
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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
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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
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1
reply
888
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
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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
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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
833
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
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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
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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
838
views
IRanges:::coverage() speedup/enchancement
Coverage IRanges Coverage IRanges
updated 14.4 years ago by ▴ 620 • written 14.4 years ago by ▴ 290
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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
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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
916
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
899
views
strand consistency with readAligned, coverage and transcriptsBy
Coverage Coverage
updated 12.6 years ago by ★ 13k • written 12.6 years ago by ▴ 220
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2
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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
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7
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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
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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