Showing : genomes • reset
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[Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred f…
Cancer Organism biomaRt GenomicFeatures genomes Cancer Organism biomaRt GenomicFeatures
updated 12.1 years ago by ▴ 660 • written 12.2 years ago by 16k
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8
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3.2k
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QuasR: how to use an indexed reference genome?
BSgenome BSgenome genomes QuasR BSgenome BSgenome genomes QuasR
updated 11.0 years ago by ▴ 350 • written 11.0 years ago by ▴ 750
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5
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Extracting all possible annotations between two genomic coordinates
genomes
7.2 years ago KB ▴ 50
0
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4
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1.5k
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rtracklayer and UCSC
rtracklayer genomes rtracklayer genomes
updated 15.0 years ago by ▴ 620 • written 15.0 years ago by ★ 6.5k
0
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8
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2.8k
views
Best practices to find intersection among variants
VariantAnnotation genomes VariantAnnotation VariantAnnotation genomes VariantAnnotation
updated 9.7 years ago by ★ 1.3k • written 9.7 years ago by ▴ 220
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2
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1.0k
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Expected value of finding a sequence (Tim Smith)
genomes genomes
updated 11.2 years ago by ▴ 10 • written 11.2 years ago by ▴ 80
0
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3
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4.8k
views
how to get gene list for given GO terms?
Pathways GO Cancer PROcess goTools genomes Pathways GO Cancer PROcess goTools genomes
updated 22 months ago by • 0 • written 12.2 years ago by ★ 7.2k
0
votes
2
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1.6k
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a workflow of population genomic operations/analysis using bioconductor
Genetics genomes Genetics genomes
updated 13.4 years ago by ★ 11k • written 13.4 years ago by ▴ 290
0
votes
2
replies
1.7k
views
Bacterial genomics
Sequencing Microarray qPCR genomes Sequencing Microarray qPCR genomes
updated 13.7 years ago by 16k • written 13.8 years ago by ▴ 30
0
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2
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1.2k
views
error from rsamtools on 1000 genomes
Cancer HapMap Rsamtools genomes Cancer HapMap Rsamtools genomes
updated 13.9 years ago by 25k • written 13.9 years ago by ▴ 100
0
votes
3
replies
2.3k
views
seqlevels in VCF objects
BSgenome BSgenome genomes BSgenome BSgenome genomes
updated 11.3 years ago by ★ 6.8k • written 11.3 years ago by ▴ 70
0
votes
2
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1.6k
views
Building custom genome in MeDIPS
BSgenome BSgenome genomes MEDIPS BSgenome BSgenome genomes MEDIPS
updated 11.6 years ago by 65k • written 11.6 years ago by ▴ 10
0
votes
2
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861
views
help on normalize only one species in two-species platform
Normalization genomes Normalization genomes
updated 19.8 years ago by ▴ 950 • written 19.8 years ago by ▴ 10
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3
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1.3k
views
Complementing alleles in a VCF
VariantAnnotation BSgenome BSgenome genomes VariantAnnotation VariantAnnotation BSgenome
updated 12.1 years ago by 25k • written 12.1 years ago by ▴ 650
0
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5
replies
2.0k
views
Rsamtools filtering bam file: RE: MEDIPS.createSet error
GO BSgenome BSgenome Rsamtools genomes MEDIPS GO BSgenome BSgenome Rsamtools genomes
updated 10.1 years ago by 25k • written 10.1 years ago by ▴ 220
1
vote
1
reply
1.6k
views
GenomeViz
Proteomics genomes Proteomics genomes
updated 8.2 years ago by • 0 • written 19.3 years ago by ▴ 80
0
votes
1
reply
2.7k
views
GenomeViz again : corrected link
Proteomics genomes Proteomics genomes
updated 19.3 years ago by ▴ 210 • written 19.3 years ago by ▴ 80
0
votes
1
reply
943
views
Defining your own chromosome annotations
geneplotter genomes geneplotter genomes
updated 19.0 years ago by 21k • written 19.0 years ago by ▴ 30
0
votes
1
reply
876
views
New bosTau4 genome
BSgenome BSgenome genomes BSgenome BSgenome genomes
updated 15.5 years ago by ▴ 500 • written 15.5 years ago by 16k
0
votes
1
reply
749
views
Reminder: Intermediate BioC Course 21-23 Jan 09
Sequencing Microarray genomes Sequencing Microarray genomes
15.3 years ago Patrick Aboyoun ★ 1.6k
0
votes
2
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642
views
comparing multiple individual genomes in bioc?
genomes genomes
updated 15.3 years ago by ★ 6.5k • written 15.3 years ago by ★ 1.1k
0
votes
2
replies
1.1k
views
biomaRt access to ensemble genomes 11 fungi_mart_11
genomes genomes
updated 12.4 years ago by ▴ 60 • written 12.4 years ago by ★ 1.6k
0
votes
1
reply
840
views
about the annotate the new genome for geneplotter/genegraph
Annotation genomes Annotation genomes
updated 14.8 years ago by ▴ 140 • written 14.8 years ago by ▴ 10
0
votes
2
replies
2.0k
views
E. coli annotation to map?
biomaRt genomes biomaRt genomes
updated 13.7 years ago by ▴ 500 • written 13.7 years ago by ▴ 40
0
votes
1
reply
730
views
Human genomic sequences
genomes genomes
updated 13.6 years ago by 6.7k • written 13.6 years ago by ▴ 30
0
votes
3
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1.0k
views
how to go from an short read alignment file to a SNPs table for population genetic analysis
genomes genomes
updated 13.4 years ago by 21k • written 13.4 years ago by ▴ 290
0
votes
8
replies
1.6k
views
Gene Lists and Genomes
GO genomes GO genomes
updated 13.0 years ago by ★ 4.2k • written 13.0 years ago by ▴ 240
0
votes
4
replies
1.1k
views
IRanges: Request for a "step" argument in runsum
Cancer IRanges genomes Cancer IRanges genomes
updated 13.0 years ago by ★ 11k • written 13.0 years ago by ▴ 100
0
votes
1
reply
739
views
IRanges: Request for a "step" argument in runsum
Cancer PROcess IRanges genomes Cancer PROcess IRanges genomes
updated 12.9 years ago by ★ 11k • written 12.9 years ago by 16k
0
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4
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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
1
reply
943
views
the procedure to annotate assembled transcriptom
annotate genomes annotate genomes
updated 12.5 years ago by 21k • written 12.5 years ago by ★ 2.0k
0
votes
1
reply
818
views
Addition of Orangutan genome to BSgenomes
Genetics BSgenome BSgenome genomes Genetics BSgenome BSgenome genomes
updated 12.5 years ago by ★ 6.8k • written 12.5 years ago by ▴ 10
0
votes
1
reply
709
views
MEDIPS R package reference genomes
genomes MEDIPS genomes MEDIPS
updated 12.4 years ago by ★ 6.8k • written 12.4 years ago by ▴ 220
0
votes
13
replies
2.3k
views
How to plot NGS data?
GO BSgenome geneplotter PROcess BSgenome genomes GO BSgenome geneplotter PROcess genomes
updated 12.2 years ago by 25k • written 12.2 years ago by ▴ 30
0
votes
2
replies
1.2k
views
Finding coding SNPs with predictCoding
SNP Annotation BSgenome ctc BSgenome cycle genomes SNP Annotation BSgenome ctc BSgenome
updated 12.1 years ago by ★ 1.7k • written 12.1 years ago by ★ 6.8k
0
votes
1
reply
1.0k
views
Course: R / Bioconductor for High-Throughput Sequence Analysis
Annotation Cancer genomes Annotation Cancer genomes
12.1 years ago Martin Morgan 25k
0
votes
1
reply
922
views
Finding coding SNPs with predictCoding
SNP Annotation BSgenome BSgenome GenomicFeatures cycle genomes SNP Annotation BSgenome
updated 12.0 years ago by ★ 1.7k • written 12.0 years ago by ★ 6.8k
0
votes
1
reply
1.5k
views
Gviz: Error plotting C.elegans ideogram
ideogram genomes Gviz ideogram genomes Gviz
11.9 years ago Michael Dondrup ▴ 550
0
votes
4
replies
1.6k
views
How can I obtain gene name from chromosome location?
Lung charm genomes Lung charm genomes
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ▴ 110
0
votes
5
replies
1.7k
views
Contrast Problem
genomes genomes
updated 11.8 years ago by 50k • written 11.8 years ago by ▴ 50
0
votes
1
reply
977
views
How to use cutome reference genome?
BSgenome BSgenome genomes MEDIPS BSgenome BSgenome genomes MEDIPS
updated 11.7 years ago by ★ 6.5k • written 11.7 years ago by ★ 13k
0
votes
2
replies
1.5k
views
VariantAnnotation: readVcf on nonmodel organism
Organism genomes Organism genomes
updated 11.6 years ago by ★ 6.8k • written 11.6 years ago by ▴ 40
0
votes
2
replies
1.2k
views
Granges averaging
genomes genomes
updated 11.6 years ago by 16k • written 11.6 years ago by ▴ 40
0
votes
3
replies
1.3k
views
VCF predictCoding(...) providing inconsistent results?
genomes genomes
11.3 years ago Murat Tasan ▴ 70
3
votes
4
replies
1.2k
views
Limit on number of sequence files for forging a BSgenome
BSgenome BSgenome genomes BSgenome BSgenome genomes
updated 11.1 years ago by ★ 6.5k • written 11.1 years ago by ▴ 220
0
votes
1
reply
1.9k
views
Help needed! What wrong with VariantAnnotation and TCGA vcfs
VariantAnnotation genomes VariantAnnotation VariantAnnotation genomes VariantAnnotation
updated 11.1 years ago by 25k • written 11.1 years ago by ▴ 340
0
votes
2
replies
1.6k
views
QuasR special case alignment
Alignment genomes QuasR Alignment genomes QuasR
updated 11.0 years ago by ▴ 340 • written 11.0 years ago by ▴ 350
0
votes
6
replies
1.6k
views
coverage on very large ReadGappedAlignmentsObject
Coverage genomes Coverage genomes
updated 11.0 years ago by 25k • written 11.0 years ago by ▴ 360
0
votes
1
reply
1.3k
views
Working with non-type strain annotation
Proteomics GO genomes Proteomics GO genomes
updated 11.0 years ago by ★ 7.2k • written 11.0 years ago by ▴ 70
0
votes
1
reply
1.5k
views
Lifting over a bam file with Rsamtools and GenomicRanges
GenomicRanges genomes GenomicRanges genomes
updated 10.6 years ago by ★ 11k • written 10.6 years ago by ★ 13k
50 results • Page 1 of 1
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Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
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Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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