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 12.1 years ago by 16k
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8
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3.2k
views
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
votes
4
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1.5k
views
rtracklayer and UCSC
rtracklayer genomes rtracklayer genomes
updated 15.0 years ago by ▴ 620 • written 15.0 years ago by ★ 6.5k
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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
views
Expected value of finding a sequence (Tim Smith)
genomes genomes
updated 11.1 years ago by ▴ 10 • written 11.1 years ago by ▴ 80
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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
views
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
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1.7k
views
Bacterial genomics
Sequencing Microarray qPCR genomes Sequencing Microarray qPCR genomes
updated 13.7 years ago by 16k • written 13.7 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 13.8 years ago by 25k • written 13.8 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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854
views
help on normalize only one species in two-species platform
Normalization genomes Normalization genomes
updated 19.7 years ago by ▴ 950 • written 19.7 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 12.0 years ago by 25k • written 12.0 years ago by ▴ 650
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votes
5
replies
1.9k
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
934
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
872
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
747
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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639
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
838
views
about the annotate the new genome for geneplotter/genegraph
Annotation genomes Annotation genomes
updated 14.7 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
728
views
Human genomic sequences
genomes genomes
updated 13.5 years ago by 6.7k • written 13.5 years ago by ▴ 30
0
votes
3
replies
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
736
views
IRanges: Request for a "step" argument in runsum
Cancer PROcess IRanges genomes Cancer PROcess IRanges genomes
updated 12.8 years ago by ★ 11k • written 12.8 years ago by 16k
0
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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
1
reply
935
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
813
views
Addition of Orangutan genome to BSgenomes
Genetics BSgenome BSgenome genomes Genetics BSgenome BSgenome genomes
updated 12.4 years ago by ★ 6.8k • written 12.5 years ago by ▴ 10
0
votes
1
reply
707
views
MEDIPS R package reference genomes
genomes MEDIPS genomes MEDIPS
updated 12.3 years ago by ★ 6.8k • written 12.3 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
917
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 • updated 11.8 years ago Michael Dondrup ▴ 550
0
votes
4
replies
1.5k
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
968
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 11.0 years ago by 25k • written 11.0 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 10.9 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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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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