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0
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13
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2.4k
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How to plot NGS data?
GO BSgenome geneplotter PROcess BSgenome genomes GO BSgenome geneplotter PROcess genomes
updated 12.3 years ago by 25k • written 12.3 years ago by ▴ 30
0
votes
8
replies
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
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
8
replies
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
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
6
replies
1.5k
views
[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 12.2 years ago by ▴ 660 • written 12.2 years ago by 16k
0
votes
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
0
votes
5
replies
1.7k
views
Contrast Problem
genomes genomes
updated 11.9 years ago by 50k • written 11.9 years ago by ▴ 50
0
votes
5
replies
1.4k
views
Extracting all possible annotations between two genomic coordinates
genomes
7.2 years ago KB ▴ 50
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
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
4
replies
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
0
votes
4
replies
1.6k
views
How can I obtain gene name from chromosome location?
Lung charm genomes Lung charm genomes
updated 11.9 years ago by ★ 13k • written 11.9 years ago by ▴ 110
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 12.9 years ago by 16k • written 12.9 years ago by ▴ 100
0
votes
3
replies
2.0k
views
Find enriched GO terms, given a list of GO terms of interest and background GO terms
Annotation GO topGO genomes Annotation GO topGO genomes
10.3 years ago Guest User ★ 13k
0
votes
3
replies
4.9k
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
2
votes
3
replies
5.1k
views
Linkage disequilibrium with 1000 Genomes/HapMap
HapMap genomes HapMap genomes
9.8 years ago enricoferrero ▴ 660
0
votes
3
replies
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
votes
3
replies
1.5k
views
Elephant shark genome
Biostrings genomes Biostrings genomes
updated 10.1 years ago by 25k • written 10.1 years ago by ★ 13k
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 13.5 years ago by 21k • written 13.5 years ago by ▴ 290
0
votes
3
replies
1.3k
views
VCF predictCoding(...) providing inconsistent results?
genomes genomes
11.3 years ago Murat Tasan ▴ 70
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
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
2
replies
1.6k
views
Building custom genome in MeDIPS
BSgenome BSgenome genomes MEDIPS BSgenome BSgenome genomes MEDIPS
updated 11.7 years ago by 65k • written 11.7 years ago by ▴ 10
0
votes
2
replies
1.5k
views
Limit on number of sequence files for forging a BSgenome
GO Cancer BSgenome BSgenome genomes GO Cancer BSgenome BSgenome genomes
11.1 years ago Hervé Pagès 16k
0
votes
2
replies
1.8k
views
Bacterial genomics
Sequencing Microarray qPCR genomes Sequencing Microarray qPCR genomes
updated 13.8 years ago by 16k • written 13.8 years ago by ▴ 30
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
2
replies
869
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
0
votes
2
replies
1.6k
views
a workflow of population genomic operations/analysis using bioconductor
Genetics genomes Genetics genomes
updated 13.5 years ago by ★ 11k • written 13.5 years ago by ▴ 290
0
votes
2
replies
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
2
replies
1.0k
views
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
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
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
2
replies
1.6k
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
2.6k
views
How to get the rsID of 4 million SNPA
ensembldb SNP SNPData genomes
written 2.2 years ago by • 0
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
2
replies
2.2k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Transcription HapMap PolyPhen SIFT convert genomes ensemblVEP Transcription HapMap SIFT
updated 10.3 years ago by ★ 6.8k • written 10.4 years ago by ▴ 30
0
votes
2
replies
647
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
1
reply
883
views
New bosTau4 genome
BSgenome BSgenome genomes BSgenome BSgenome genomes
updated 15.6 years ago by ▴ 500 • written 15.6 years ago by 16k
1
vote
1
reply
1.7k
views
GenomeViz
Proteomics genomes Proteomics genomes
updated 8.3 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
947
views
Defining your own chromosome annotations
geneplotter genomes geneplotter genomes
updated 19.1 years ago by 21k • written 19.1 years ago by ▴ 30
0
votes
1
reply
756
views
Reminder: Intermediate BioC Course 21-23 Jan 09
Sequencing Microarray genomes Sequencing Microarray genomes
15.4 years ago Patrick Aboyoun ★ 1.6k
0
votes
1
reply
849
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
1
reply
735
views
Human genomic sequences
genomes genomes
updated 13.6 years ago by 6.7k • written 13.6 years ago by ▴ 30
0
votes
1
reply
744
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
votes
1
reply
947
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
820
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
713
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
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters by anne-laure • 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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