Showing : coverage • reset
6
votes
3
replies
2.4k
views
how does coverage() works
biostrings coverage rle iranges
7.9 years ago likeeatingpizza ▴ 10
6
votes
0
replies
2.8k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma
17.8 years ago • updated 8.3 years ago Gordon Smyth 50k
5
votes
2
replies
3.1k
views
Gviz - show plus and minus strand from a bam
Sequencing Coverage Gviz Sequencing Coverage Gviz
updated 10.5 years ago by ★ 1.6k • written 10.5 years ago by ▴ 510
5
votes
3
replies
1.8k
views
Calling coverage on GRanges object yields small negative values
granges coverage
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 10
4
votes
2
replies
1.6k
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 7.3 years ago by • 0 • written 7.3 years ago by ▴ 40
3
votes
2
replies
1.9k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 6.2 years ago by 16k • written 6.2 years ago by ▴ 10
3
votes
4
replies
1.0k
views
Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
2.6 years ago Rui ▴ 10
2
votes
6
replies
2.8k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 30
2
votes
3
replies
1.6k
views
Is there an easy way to extend coverage to seqlengths and fill with zeroes?
coverage s4vectors seqlengths
8.2 years ago liz.ingsimmons ▴ 140
2
votes
5
replies
1.9k
views
GOseq: count bias correction variations?
Coverage goseq
updated 7.1 years ago by 50k • written 9.8 years ago by ▴ 40
2
votes
6
replies
1.4k
views
Using edgeR with "traditional" coverage data?
edger rnaseq coverage
updated 8.0 years ago by ★ 7.9k • written 8.0 years ago by • 0
1
vote
3
replies
3.9k
views
Blast analysis of two sequences in R
Coverage Coverage
updated 10.0 years ago by 25k • written 10.0 years ago by ▴ 100
1
vote
2
replies
1.5k
views
Gviz off-by-one with STAR BAM
gviz off-by-one STAR BAM coverage
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
1
vote
2
replies
2.6k
views
"Normalising" GRanges coverage object
Coverage GO Gviz Coverage GO Gviz
updated 9.7 years ago by ★ 7.9k • written 9.7 years ago by ▴ 350
1
vote
0
replies
1.9k
views
pileup coverage from BAM file
Coverage Cancer IRanges GenomicRanges Coverage Cancer IRanges GenomicRanges
11.2 years ago Martin Morgan 25k
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
1
vote
2
replies
1.9k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 90
1
vote
2
replies
1.5k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 4.6 years ago by ★ 11k • written 7.1 years ago by ▴ 10
0
votes
0
replies
719
views
X:Map and 1.0 ST Gene Arrays, Introns
Coverage probe Coverage probe
15.8 years ago Thomas Hampton ▴ 750
0
votes
3
replies
1.2k
views
gene2pathway retrain: which model is more complete?
Genetics Coverage biomaRt gene2pathway Genetics Coverage biomaRt gene2pathway
13.7 years ago Bogdan ▴ 50
0
votes
1
reply
893
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
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
840
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
5
replies
1.9k
views
read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 14.7 years ago by 25k • written 14.7 years ago by ▴ 40
0
votes
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
1
reply
842
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
0
votes
1
reply
3.2k
views
color key - heatmap.2
Coverage Coverage
updated 14.2 years ago by 21k • written 14.2 years ago by ▴ 10
0
votes
0
replies
916
views
request: calculate coverage with weight on RangedData object
Coverage Cancer IRanges Coverage Cancer IRanges
14.1 years ago Janet Young ▴ 740
0
votes
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
2
replies
915
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
votes
3
replies
3.3k
views
from RefSeq to GO terms / gene symbol to geneID
Proteomics Coverage Annotation GO Proteomics Coverage Annotation GO
16.9 years ago Simon Lin ▴ 270
0
votes
0
replies
1.5k
views
New Quantian releases with almost all of CRAN / BioC
Coverage Visualization GUI Coverage Visualization GUI
18.2 years ago Dirk Eddelbuettel ▴ 80
0
votes
1
reply
1.4k
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
0
replies
5.1k
views
Reading GFF files into R and GenomeGraphs
Coverage Annotation Visualization convert GLAD GenomeGraphs rtracklayer IRanges Coverage
14.7 years ago Michael Dondrup ▴ 140
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
0
replies
865
views
from RefSeq GI protein identifiers to GO terms
Proteomics Coverage GO Proteomics Coverage GO
16.9 years ago Lina Hultin-Rosenberg ▴ 80
0
votes
0
replies
930
views
Ensembl mart release 54: Useful information
Coverage zebrafish Coverage zebrafish
15.0 years ago Rhoda Kinsella ▴ 660
0
votes
2
replies
1.1k
views
raw counts for edgeR
Coverage Coverage
updated 13.0 years ago by 21k • written 13.0 years ago by ★ 1.3k
0
votes
0
replies
968
views
rtracklayer
Coverage Cancer Coverage Cancer
13.0 years ago Michael Lawrence ★ 11k
0
votes
1
reply
1.3k
views
A CGH platform question
SNP Genetics Coverage CGH affy SNP Genetics Coverage CGH affy
updated 15.4 years ago by ★ 2.4k • written 15.4 years ago by ▴ 70
0
votes
3
replies
2.5k
views
Any package to calculate NGS coverage and plot it?
Coverage Coverage
12.9 years ago Xiaohui Wu ▴ 280
0
votes
4
replies
1.3k
views
IRanges: Request for a "step" argument in runsum
Coverage Annotation Cancer PROcess IRanges genomes Coverage Annotation Cancer PROcess
updated 12.8 years ago by 16k • written 12.9 years ago by ▴ 100
0
votes
8
replies
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
votes
1
reply
903
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
17
replies
2.2k
views
Coverage by base
Coverage Coverage
12.6 years ago rohan bareja ▴ 200
0
votes
2
replies
860
views
Coverage of reads in 3'UTR
Coverage Coverage
12.6 years ago • updated 12.5 years ago rohan bareja ▴ 200
0
votes
0
replies
965
views
Using DESeq with ChIP-seq data - all or non-redundant reads?
Coverage Kidney DESeq Coverage Kidney DESeq
12.5 years ago Ivan Gregoretti ▴ 310
0
votes
0
replies
928
views
Normalization in Coverage
Coverage Normalization Coverage Normalization
12.5 years ago rohan bareja ▴ 200
0
votes
3
replies
1.4k
views
Normalization in Coverage
Coverage Normalization Coverage Normalization
12.5 years ago rohan bareja ▴ 200
0
votes
0
replies
1.5k
views
easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
10.1 years ago Guest User ★ 13k
50 results • Page 1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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