Showing : Coverage • reset
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[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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17
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2.4k
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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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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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11
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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
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[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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10
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1.8k
views
Calculate Outer Positions of GappedAlignmentPairs
Coverage GenomicRanges Coverage GenomicRanges
updated 11.7 years ago by ★ 11k • written 11.7 years ago by ★ 1.5k
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10
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1.6k
views
Computing the coverage on a bamfile with a huge amount of seqlevels
Coverage Coverage
updated 11.1 years ago by 16k • written 11.1 years ago by ▴ 360
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8
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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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8
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1.9k
views
Filtering BAM files by start position for VariantTools
Coverage Cancer cycle VariantTools Coverage Cancer cycle VariantTools
updated 11.3 years ago by ▴ 250 • written 11.3 years ago by 25k
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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
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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
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7
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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
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6
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1.8k
views
coverage on very large ReadGappedAlignmentsObject
Coverage genomes Coverage genomes
updated 11.6 years ago by 25k • written 11.6 years ago by ▴ 360
2
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6
replies
1.6k
views
Using edgeR with "traditional" coverage data?
edger rnaseq coverage
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by • 0
2
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6
replies
3.0k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 30
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6
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1.3k
views
readGapppedAlignmentpairs questions
Coverage PROcess Coverage PROcess
updated 12.5 years ago by ★ 3.6k • written 12.5 years ago by ▴ 250
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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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6
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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
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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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5
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2.1k
views
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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5
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2.2k
views
ensemblVEP: passing on coverage / frequency information
Coverage VariantTools ensemblVEP Coverage VariantTools ensemblVEP
updated 11.7 years ago by ★ 6.8k • written 11.7 years ago by ★ 13k
0
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5
replies
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
2
votes
5
replies
2.2k
views
GOseq: count bias correction variations?
Coverage goseq
updated 7.6 years ago by 52k • written 10.4 years ago by ▴ 40
0
votes
5
replies
3.8k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Annotation graph Gviz Coverage Annotation graph Gviz
updated 10.6 years ago by ▴ 130 • written 10.6 years ago by ▴ 350
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5
replies
1.9k
views
Visualization of alignments with mismatch bases
SNP Coverage Alignment Visualization ggbio SNP Coverage Alignment Visualization ggbio
updated 11.8 years ago by ▴ 420 • written 11.8 years ago by ★ 11k
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4
replies
1.6k
views
AlignmentsTrack empty plot
Coverage RNASeq plot Gviz
updated 22 months ago by 67k • written 3.3 years ago by • 0
3
votes
4
replies
1.3k
views
Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
3.2 years ago Rui ▴ 10
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4
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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
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4
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1.9k
views
Rsamtools: Realloc integer overflow?
Coverage Coverage
updated 11.5 years ago by 25k • written 11.5 years ago by ★ 11k
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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
0
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4
replies
1.4k
views
IRanges: Request for a "step" argument in runsum
Coverage Annotation Cancer PROcess IRanges genomes Coverage Annotation Cancer PROcess
updated 13.4 years ago by 16k • written 13.4 years ago by ▴ 100
0
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4
replies
2.0k
views
htSeqTools errors
Coverage htSeqTools Coverage htSeqTools
updated 12.8 years ago by ★ 6.8k • written 12.8 years ago by ▴ 80
0
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3
replies
1.4k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
6.1 years ago faramer86 • 0
0
votes
3
replies
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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3
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1.4k
views
gene2pathway retrain: which model is more complete?
Genetics Coverage biomaRt gene2pathway Genetics Coverage biomaRt gene2pathway
14.3 years ago Bogdan ▴ 50
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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3
replies
1.6k
views
Normalization in Coverage
Coverage Normalization Coverage Normalization
13.1 years ago rohan bareja ▴ 200
0
votes
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
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
5
votes
3
replies
1.9k
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 9.6 years ago by 16k • written 9.6 years ago by ▴ 10
0
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3
replies
2.7k
views
Any package to calculate NGS coverage and plot it?
Coverage Coverage
13.5 years ago Xiaohui Wu ▴ 280
0
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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
0
votes
3
replies
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
0
votes
3
replies
1.3k
views
Some more rtracklayer questions (re: WIG and .VSTEP files)
Coverage rtracklayer GenomicRanges Coverage rtracklayer GenomicRanges
updated 13.0 years ago by ★ 11k • written 13.0 years ago by ★ 4.2k
1
vote
3
replies
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
1
vote
3
replies
4.2k
views
Blast analysis of two sequences in R
Coverage Coverage
updated 10.6 years ago by 25k • written 10.6 years ago by ▴ 100
0
votes
3
replies
1.3k
views
speed of runmed on SimpleRleList
Coverage Cancer Coverage Cancer
updated 11.8 years ago by 16k • written 11.8 years ago by ▴ 740
2
votes
3
replies
1.7k
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage s4vectors seqlengths
8.8 years ago liz.ingsimmons ▴ 140
0
votes
2
replies
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
5
votes
2
replies
3.3k
views
Gviz - show plus and minus strand from a bam
Sequencing Coverage Gviz Sequencing Coverage Gviz
updated 11.1 years ago by ★ 1.6k • written 11.1 years ago by ▴ 510
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…
Votes
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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