Showing : Coverage • reset
0
votes
2
replies
7.5k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 12.4 years ago by ★ 11k • written 12.4 years ago by 16k
0
votes
2
replies
6.7k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.9 years ago by ▴ 20 • written 4.0 years ago by • 0
0
votes
0
replies
6.1k
views
Reading GFF files into R and GenomeGraphs
Coverage Annotation Visualization convert GLAD GenomeGraphs rtracklayer IRanges Coverage
16.6 years ago Michael Dondrup ▴ 140
0
votes
16
replies
5.3k
views
subset a RleList using GRanges object?
Coverage Cancer IRanges Coverage Cancer IRanges
updated 12.3 years ago by 16k • written 12.3 years ago by ▴ 740
0
votes
11
replies
5.2k
views
creating GRanges and reading BAM files
Coverage convert Coverage convert
updated 14.0 years ago by ▴ 80 • written 14.0 years ago by ▴ 70
0
votes
0
replies
5.2k
views
Bioconductor 2.13 is released
BiocViews aCGH SNP Transcription Sequencing miRNA Microarray Genetics Proteomics Coverage
12.4 years ago Dan Tenenbaum ★ 8.2k
1
vote
3
replies
4.9k
views
Blast analysis of two sequences in R
Coverage Coverage
updated 11.9 years ago by 25k • written 11.9 years ago by ▴ 100
0
votes
2
replies
4.7k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 10.7 years ago by • 0 • written 12.9 years ago by ★ 8.2k
0
votes
0
replies
4.7k
views
Bioconductor 2.14 is released
BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage
11.9 years ago Dan Tenenbaum ★ 8.2k
0
votes
3
replies
4.6k
views
from RefSeq to GO terms / gene symbol to geneID
Proteomics Coverage Annotation GO Proteomics Coverage Annotation GO
18.8 years ago • updated 18.7 years ago Simon Lin ▴ 270
0
votes
3
replies
4.5k
views
DESeq estimateDispersions
Coverage DESeq Coverage DESeq
updated 12.9 years ago by ★ 3.8k • written 12.9 years ago by ▴ 330
0
votes
5
replies
4.4k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Annotation graph Gviz Coverage Annotation graph Gviz
updated 11.9 years ago by ▴ 130 • written 11.9 years ago by ▴ 350
0
votes
8
replies
4.0k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 14.6 years ago by 16k • written 14.6 years ago by ▴ 740
0
votes
17
replies
4.0k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ▴ 330
6
votes
0
replies
3.9k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma
19.6 years ago • updated 10.1 years ago Gordon Smyth 53k
5
votes
2
replies
3.7k
views
Gviz - show plus and minus strand from a bam
Sequencing Coverage Gviz Sequencing Coverage Gviz
updated 12.3 years ago by ★ 1.6k • written 12.3 years ago by ▴ 510
6
votes
3
replies
3.7k
views
how does coverage() works
biostrings coverage rle iranges
9.8 years ago likeeatingpizza ▴ 10
0
votes
1
reply
3.7k
views
color key - heatmap.2
Coverage Coverage
updated 16.0 years ago by 21k • written 16.0 years ago by ▴ 10
0
votes
0
replies
3.7k
views
Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
13.4 years ago Dan Tenenbaum ★ 8.2k
0
votes
1
reply
3.6k
views
displaying coverage RNAseq Gviz
RNASeq Coverage Gviz RNASeq Coverage Gviz
11.8 years ago florian.hahne@novartis.com ★ 1.6k
2
votes
6
replies
3.6k
views
Shrink or Expand RLE
RLE iranges granges coverage
updated 10.9 years ago by 25k • written 10.9 years ago by ▴ 30
1
vote
2
replies
3.5k
views
"Normalising" GRanges coverage object
Coverage GO Gviz Coverage GO Gviz
updated 11.6 years ago by ★ 7.9k • written 11.6 years ago by ▴ 350
0
votes
6
replies
3.5k
views
Displaying very deep coverage in Gviz
Coverage Gviz Coverage Gviz
updated 11.8 years ago by ★ 1.6k • written 11.8 years ago by ▴ 130
0
votes
4
replies
3.4k
views
Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 2.4 years ago by • 0 • written 11.5 years ago by ★ 13k
0
votes
17
replies
3.2k
views
Coverage by base
Coverage Coverage
14.4 years ago rohan bareja ▴ 200
0
votes
1
reply
3.2k
views
Integer overflow when summing an 'integer' Rle
Coverage GO Cancer convert IRanges Coverage GO Cancer convert IRanges
updated 13.5 years ago by ★ 1.2k • written 13.5 years ago by ★ 6.8k
0
votes
6
replies
3.2k
views
Gviz: axes related parameters
Coverage Gviz Coverage Gviz
updated 12.0 years ago by ★ 13k • written 12.0 years ago by ▴ 170
0
votes
3
replies
3.2k
views
Coverage of reads per base position from BAM files
Coverage GO Coverage GO
updated 13.7 years ago by 25k • written 13.7 years ago by ★ 13k
0
votes
2
replies
3.1k
views
BH vs BY in p.adjust + FDR interpretation
Coverage limma Coverage limma
updated 10.1 years ago by 53k • written 19.6 years ago by ▴ 50
0
votes
3
replies
3.1k
views
Any package to calculate NGS coverage and plot it?
Coverage Coverage
14.8 years ago Xiaohui Wu ▴ 280
0
votes
1
reply
3.0k
views
Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
wiggleplotr bigwig coverage ngs
updated 8.4 years ago by ▴ 30 • written 8.4 years ago by • 0
0
votes
5
replies
2.9k
views
ensemblVEP: passing on coverage / frequency information
Coverage VariantTools ensemblVEP Coverage VariantTools ensemblVEP
updated 12.9 years ago by ★ 6.8k • written 12.9 years ago by ★ 13k
1
vote
3
replies
2.8k
views
views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 12.0 years ago by 16k • written 12.0 years ago by ★ 11k
0
votes
5
replies
2.8k
views
SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
biseq RRBS SAAP-BS coverage
10.9 years ago maria.maqueda • 0
2
votes
5
replies
2.7k
views
GOseq: count bias correction variations?
Coverage goseq
updated 8.9 years ago by 53k • written 11.6 years ago by ▴ 40
3
votes
2
replies
2.7k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 8.1 years ago by 16k • written 8.1 years ago by ▴ 10
0
votes
2
replies
2.7k
views
Coverage vs GC bias - how to?
Coverage BSgenome BSgenome IRanges Coverage BSgenome BSgenome IRanges
updated 15.5 years ago by ▴ 590 • written 15.5 years ago by ▴ 100
0
votes
2
replies
2.7k
views
Gviz - Visualize Reads - Color by Presence of Junction?
Coverage Gviz Coverage Gviz
updated 12.3 years ago by ▴ 750 • written 12.3 years ago by ▴ 120
0
votes
1
reply
2.6k
views
Bioconductor Digest, Vol 120, Issue 12
Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy
13.1 years ago Matthew Thornton ▴ 390
1
vote
2
replies
2.5k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 10.7 years ago by 25k • written 10.7 years ago by ▴ 90
0
votes
0
replies
2.5k
views
problem reading bigwig files with rtracklayer from Ensembl mitochondrion chromosome name
Coverage Annotation rtracklayer Coverage Annotation rtracklayer
11.7 years ago Marco Blanchette ▴ 220
0
votes
8
replies
2.5k
views
CIGAR-aware coverage
Coverage IRanges Coverage IRanges
updated 12.0 years ago by ★ 11k • written 12.0 years ago by ▴ 30
0
votes
2
replies
2.4k
views
Wig files?
Coverage Coverage
updated 13.7 years ago by ★ 11k • written 13.7 years ago by ▴ 230
0
votes
5
replies
2.4k
views
read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 16.5 years ago by 25k • written 16.5 years ago by ▴ 40
0
votes
10
replies
2.4k
views
Calculate Outer Positions of GappedAlignmentPairs
Coverage GenomicRanges Coverage GenomicRanges
updated 13.0 years ago by ★ 11k • written 13.0 years ago by ★ 1.6k
0
votes
1
reply
2.4k
views
compilation failed for package \'IRanges\' @str_utils.c(152) identifier \"timezone\" is undefined
Coverage IRanges Coverage IRanges
updated 13.4 years ago by ★ 8.2k • written 13.4 years ago by ★ 13k
0
votes
5
replies
2.3k
views
Visualization of alignments with mismatch bases
SNP Coverage Alignment Visualization ggbio SNP Coverage Alignment Visualization ggbio
updated 13.0 years ago by ▴ 420 • written 13.0 years ago by ★ 11k
0
votes
4
replies
2.3k
views
htSeqTools errors
Coverage htSeqTools Coverage htSeqTools
updated 14.1 years ago by ★ 6.8k • written 14.1 years ago by ▴ 80
0
votes
8
replies
2.3k
views
Filtering BAM files by start position for VariantTools
Coverage Cancer cycle VariantTools Coverage Cancer cycle VariantTools
updated 12.6 years ago by ▴ 250 • written 12.6 years ago by 25k
4
votes
2
replies
2.3k
views
bamsignals - bamcoverage has no strand-specific option??
BAM bamsignals Coverage
updated 9.1 years ago by • 0 • written 9.1 years ago by ▴ 40
152 results • Page 1 of 4
Recent ...
Replies
Comment: Quick two questions on limpa by JKim • 0
Thank you very much for taking the time to offer your advice and comments. I truly appreciate them. Best regards, J Kim
Answer: Convergence Issues and Model Selection DESeq2 by Michael Love 43k
You could try `glmGamPoi` fitting via `fitType`: https://github.com/thelovelab/DESeq2/blob/devel/man/DESeq.Rd#L10 This is a more rece…
Answer: Limma-voom sample weights and impact on DEG numbers by Taimor • 0
<a href="https://tntsimregisteer.com/">talk n text sim registration</a> officially provides three safe and authorized ways to register sim…
Answer: Quick two questions on limpa by Gordon Smyth 53k
Thanks for your questions about limpa. The short answer is that you should use the default settings of the readSpectronaut() function. The…
Comment: ComplexHeatmap removes row labels if annotation is added by RosaliaSchulist99 • 0
thanks for sharing https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#automatic-adjustment-to-the-main-heatmap
Votes
Answer: Quick two questions on limpa
Answer: Quick two questions on limpa
Comment: tximeta cannot open annotation gtf?
Answer: tximeta cannot open annotation gtf?
Comment: Question about using LRT test for time course experiments with DESeq2
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.3k
Popular Question to helucro ▴ 70
Teacher to ATpoint ★ 5.0k
Teacher to Michael Love 43k
Locations • All
United States, 20 minutes ago
United States, 1 hour ago
USA, 1 hour ago
Chile, 1 hour ago
United States, 1 hour ago
Traffic: 2416 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6