Showing : Coverage • reset
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Coverage by base
Coverage Coverage
13.2 years ago • updated 13.1 years ago rohan bareja ▴ 200
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10
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1.5k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Microarray Coverage Microarray Coverage
11.5 years ago Thomas Girke ★ 1.7k
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5
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2.1k
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read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 15.3 years ago by 25k • written 15.3 years ago by ▴ 40
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3
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views
gene2pathway retrain: which model is more complete?
Genetics Coverage biomaRt gene2pathway Genetics Coverage biomaRt gene2pathway
14.3 years ago Bogdan ▴ 50
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6
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2.9k
views
Displaying very deep coverage in Gviz
Coverage Gviz Coverage Gviz
updated 10.6 years ago by ★ 1.6k • written 10.6 years ago by ▴ 130
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16
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4.4k
views
subset a RleList using GRanges object?
Coverage Cancer IRanges Coverage Cancer IRanges
updated 11.0 years ago by 16k • written 11.0 years ago by ▴ 740
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3
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2.7k
views
Any package to calculate NGS coverage and plot it?
Coverage Coverage
13.5 years ago Xiaohui Wu ▴ 280
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3
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3.6k
views
from RefSeq to GO terms / gene symbol to geneID
Proteomics Coverage Annotation GO Proteomics Coverage Annotation GO
17.5 years ago • updated 17.4 years ago Simon Lin ▴ 270
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2
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4.0k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 9.4 years ago by • 0 • written 11.7 years ago by ★ 8.2k
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3
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1.6k
views
Normalization in Coverage
Coverage Normalization Coverage Normalization
13.1 years ago rohan bareja ▴ 200
0
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2
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958
views
Coverage of reads in 3'UTR
Coverage Coverage
13.1 years ago rohan bareja ▴ 200
0
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2
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1.8k
views
mr.edgeR tests in MEDIPS package
Coverage MEDIPS Coverage MEDIPS
updated 10.6 years ago by ▴ 280 • written 10.6 years ago by ▴ 10
1
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3
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2.4k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 10.7 years ago by 16k • written 10.7 years ago by ★ 11k
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2
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1.1k
views
next-generation sequencing and embryogenisis
Sequencing SAGE Coverage Sequencing SAGE Coverage
updated 14.4 years ago by ▴ 330 • written 14.4 years ago by ▴ 20
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3
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1.2k
views
Deleting object rows while looping - II
Coverage Alignment Cancer PROcess Coverage Alignment Cancer PROcess
updated 11.6 years ago by ★ 13k • written 11.6 years ago by 16k
1
vote
2
replies
1.7k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 5.2 years ago by ★ 11k • written 7.7 years ago by ▴ 10
0
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8
replies
2.0k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 10.8 years ago by ★ 11k • written 10.8 years ago by ▴ 30
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5
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2.3k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
9.6 years ago maria.maqueda • 0
0
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2
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1.2k
views
using RUnit inspect() feature in package testing
Coverage Coverage
updated 12.3 years ago by ▴ 750 • written 12.3 years ago by ★ 1.1k
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4
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3.0k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 13 months ago by • 0 • written 10.2 years ago by ★ 13k
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8
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3.5k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 13.3 years ago by 16k • written 13.3 years ago by ▴ 740
0
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2
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4.7k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.7 years ago by ▴ 20 • written 2.7 years ago by • 0
0
votes
2
replies
6.8k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 11.1 years ago by ★ 11k • written 11.1 years ago by 16k
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7
replies
1.7k
views
export Views of Rle in rtracklayer
Coverage rtracklayer Coverage rtracklayer
updated 13.0 years ago by ★ 11k • written 13.0 years ago by ▴ 190
6
votes
3
replies
2.9k
views
how does coverage() works
biostrings coverage rle iranges
8.5 years ago likeeatingpizza ▴ 10
0
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17
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3.0k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ▴ 330
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3
replies
4.1k
views
DESeq estimateDispersions
Coverage DESeq Coverage DESeq
updated 11.6 years ago by ★ 3.8k • written 11.6 years ago by ▴ 330
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3
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2.7k
views
Coverage of reads per base position from BAM files
Coverage GO Coverage GO
updated 12.4 years ago by 25k • written 12.4 years ago by ★ 13k
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2
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2.4k
views
Coverage vs GC bias - how to?
Coverage BSgenome BSgenome IRanges Coverage BSgenome BSgenome IRanges
updated 14.2 years ago by ▴ 590 • written 14.2 years ago by ▴ 100
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2
replies
2.6k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma Coverage limma
updated 8.9 years ago by 52k • written 18.4 years ago by ▴ 50
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11
replies
4.4k
views
creating GRanges and reading BAM files
Coverage convert Coverage convert
updated 12.7 years ago by ▴ 80 • written 12.8 years ago by ▴ 70
0
votes
3
replies
1.6k
views
Deleting object rows while looping - II
Coverage Alignment PROcess Coverage Alignment PROcess
updated 11.6 years ago by 25k • written 11.6 years ago by ▴ 90
0
votes
6
replies
1.3k
views
readGapppedAlignmentpairs questions
Coverage PROcess Coverage PROcess
updated 12.5 years ago by ★ 3.6k • written 12.5 years ago by ▴ 250
0
votes
2
replies
1.6k
views
[devteam-bioc] Can you give me a sample to calculate the Read Depth with Rsamtools?
Coverage Cancer Rsamtools Coverage Cancer Rsamtools
updated 11.9 years ago by ▴ 10 • written 11.9 years ago by 25k
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6
replies
2.6k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 10.8 years ago by ★ 13k • written 10.8 years ago by ▴ 170
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1
reply
1.3k
views
loop over IRanges spaces
Coverage convert rtracklayer ASSIGN Coverage convert rtracklayer ASSIGN
updated 14.6 years ago by ★ 11k • written 14.6 years ago by ▴ 60
0
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1
reply
1.0k
views
tiling/SNP microarrays
SNP Coverage tilingArray SNP Coverage tilingArray
updated 18.4 years ago by 21k • written 18.4 years ago by ▴ 10
0
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1
reply
3.3k
views
color key - heatmap.2
Coverage Coverage
updated 14.7 years ago by 21k • written 14.7 years ago by ▴ 10
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2
replies
2.0k
views
Wig files?
Coverage Coverage
updated 12.4 years ago by ★ 11k • written 12.4 years ago by ▴ 230
0
votes
1
reply
941
views
"islands" and number of reads in the island in package chipseq/ShortRead
ChIPSeq Coverage chipseq ChIPSeq Coverage chipseq
updated 15.0 years ago by ★ 6.5k • written 15.0 years ago by ▴ 40
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votes
2
replies
1.2k
views
IRanges:::coverage() speedup/enchancement
Coverage IRanges Coverage IRanges
updated 15.0 years ago by ▴ 290 • written 15.0 years ago by ★ 1.6k
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votes
4
replies
1.3k
views
Opinions on array design, normalization, and linear modeling with LIMMA
Sequencing Coverage Normalization limma Sequencing Coverage Normalization limma
updated 17.1 years ago by ▴ 60 • written 17.1 years ago by ▴ 890
0
votes
1
reply
944
views
IRanges:::coverage() speedup/enchancement
Coverage IRanges Coverage IRanges
updated 15.0 years ago by ▴ 620 • written 15.0 years ago by ▴ 290
0
votes
1
reply
1.5k
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 11.0 years ago by ▴ 320 • written 11.0 years ago by 52k
0
votes
1
reply
908
views
IRanges: the width argument of the coverage function
Coverage Coverage
updated 12.4 years ago by 16k • written 12.4 years ago by ★ 1.2k
0
votes
6
replies
1.7k
views
IRanges coverage integer limit?
Coverage IRanges Coverage IRanges
updated 12.4 years ago by 16k • written 12.4 years ago by ★ 1.2k
0
votes
1
reply
1.0k
views
seqbias : how to correct weight of mapped short reads?
Coverage IRanges seqbias Coverage IRanges seqbias
updated 12.6 years ago by 25k • written 12.6 years ago by ▴ 230
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1
reply
1.0k
views
strand consistency with readAligned, coverage and transcriptsBy
Coverage Coverage
updated 13.2 years ago by ★ 13k • written 13.2 years ago by ▴ 220
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votes
2
replies
1.4k
views
interoperability between IRanges/ShortRead and rtracklayer
Coverage rtracklayer IRanges Coverage rtracklayer IRanges
updated 15.5 years ago by ★ 1.6k • written 15.5 years ago by ▴ 150
0
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7
replies
1.8k
views
Amplicon and exon level read counts and GC content
Coverage Cancer Coverage Cancer
updated 12.5 years ago by 25k • written 12.5 years ago by ▴ 440
50 results • Page 1 of 1
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Comment: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You can examine the structure of a `DelayedMatrix` by calling the `showtree()` function. For example: ``` library(scRNAseq) X <- fetchData…
Comment: lfcShrink and alpha value by cropero • 0
Thank you so much! Would that be equivalent to perform `res <- results(dds, contrast = c("conditions", "wild_type_114_2_no_carbon", "wild_t…
Comment: pathview - multiple states by Philippine • 0
Thank you! Here a subset of genes that really works with "ame04145". data <- data.frame( EntrezID = c(100577548, 100577764, 406…
Comment: pathview - multiple states by Guido Hooiveld ★ 4.1k
A quick comment after I copied/pasted your code: when using `geneList1` in the 3rd code chunk I do **not** get a nice plot... I rather got …
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Adam • 0
Hi Aaron, Thanks a lot for your help! As you mentioned, I checked my data and it is "DelayedMatrix". I don't know the detailed differe…
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Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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