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
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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 7.0 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
718
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
892
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
841
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
3.1k
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
914
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
929
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 12.8 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
963
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
927
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
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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