Showing : genomes • reset
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Useful information about Ensembl release 71 mart databases
zebrafish PolyPhen SIFT affy genomes zebrafish PolyPhen SIFT affy genomes
12.7 years ago Thomas Maurel ▴ 800
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1.7k
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Biostatistician position in London
Cancer genomes Cancer genomes
12.7 years ago Kathi Zarnack ▴ 110
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2
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1.8k
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Limit on number of sequence files for forging a BSgenome
GO Cancer BSgenome BSgenome genomes GO Cancer BSgenome BSgenome genomes
12.7 years ago Hervé Pagès 16k
3
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4
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1.6k
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Limit on number of sequence files for forging a BSgenome
BSgenome BSgenome genomes BSgenome BSgenome genomes
updated 12.7 years ago by ★ 6.5k • written 12.7 years ago by ▴ 220
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2
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1.4k
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Expected value of finding a sequence (Tim Smith)
genomes genomes
updated 12.8 years ago by ▴ 10 • written 12.8 years ago by ▴ 80
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1.6k
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Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands
zebrafish biomaRt ideogram genomes zebrafish biomaRt ideogram genomes
12.8 years ago florian.hahne@novartis.com ★ 1.6k
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Useful information about Ensembl release 70 mart databases
genomes genomes
12.9 years ago Thomas Maurel ▴ 800
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3
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1.7k
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VCF predictCoding(...) providing inconsistent results?
genomes genomes
12.9 years ago Murat Tasan ▴ 70
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3
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3.1k
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seqlevels in VCF objects
BSgenome BSgenome genomes BSgenome BSgenome genomes
updated 12.9 years ago by ★ 6.8k • written 12.9 years ago by ▴ 70
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2
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1.5k
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Granges averaging
genomes genomes
updated 13.2 years ago by 16k • written 13.2 years ago by ▴ 40
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2
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1.9k
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VariantAnnotation: readVcf on nonmodel organism
Organism genomes Organism genomes
updated 13.2 years ago by ★ 6.8k • written 13.2 years ago by ▴ 40
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2
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2.0k
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Building custom genome in MeDIPS
BSgenome BSgenome genomes MEDIPS BSgenome BSgenome genomes MEDIPS
updated 13.2 years ago by 68k • written 13.2 years ago by ▴ 10
0
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regarding mapping package
Cancer genomes Rsubread gmapR Cancer genomes Rsubread gmapR
13.3 years ago Martin Morgan 25k
0
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1
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1.2k
views
How to use cutome reference genome?
BSgenome BSgenome genomes MEDIPS BSgenome BSgenome genomes MEDIPS
updated 13.3 years ago by ★ 6.5k • written 13.3 years ago by ★ 13k
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1.6k
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Job: Research Associate in Bioinformatics, Cambridge, UK
Sequencing genomes Sequencing genomes
13.3 years ago Krys Kelly ▴ 270
0
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5
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2.0k
views
Contrast Problem
genomes genomes
updated 13.4 years ago by 53k • written 13.4 years ago by ▴ 50
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4
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2.2k
views
How can I obtain gene name from chromosome location?
Lung charm genomes Lung charm genomes
updated 13.4 years ago by ★ 13k • written 13.4 years ago by ▴ 110
0
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1
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1.9k
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Gviz: Error plotting C.elegans ideogram
ideogram genomes Gviz ideogram genomes Gviz
13.5 years ago Michael Dondrup ▴ 550
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1.6k
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[Engineers for ensemblgenomes.org #251937] BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info …
Drosophila melanogaster TranscriptDb biomaRt GenomicFeatures genomes Drosophila melanogaster
13.5 years ago Malcolm Cook ★ 1.6k
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1.2k
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Finding coding SNPs with predictCoding
SNP Annotation BSgenome BSgenome GenomicFeatures cycle genomes SNP Annotation BSgenome
updated 13.6 years ago by ★ 1.7k • written 13.6 years ago by ★ 6.8k
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3
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Complementing alleles in a VCF
VariantAnnotation BSgenome BSgenome genomes VariantAnnotation VariantAnnotation BSgenome
updated 13.6 years ago by 25k • written 13.6 years ago by ▴ 650
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[Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred f…
Cancer Organism biomaRt genomes Cancer Organism biomaRt genomes
13.7 years ago Malcolm Cook ★ 1.6k
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1
reply
1.2k
views
Course: R / Bioconductor for High-Throughput Sequence Analysis
Annotation Cancer genomes Annotation Cancer genomes
13.7 years ago Martin Morgan 25k
0
votes
2
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1.5k
views
Finding coding SNPs with predictCoding
SNP Annotation BSgenome ctc BSgenome cycle genomes SNP Annotation BSgenome ctc BSgenome
updated 13.7 years ago by ★ 1.7k • written 13.7 years ago by ★ 6.8k
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2.0k
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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 13.7 years ago by ▴ 660 • written 13.8 years ago by 16k
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1.6k
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Job Announcement: Genome Informatics
Sequencing Genetics genomes Sequencing Genetics genomes
13.7 years ago Jenny Drnevich ★ 2.0k
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3
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6.4k
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how to get gene list for given GO terms?
Pathways GO Cancer PROcess goTools genomes Pathways GO Cancer PROcess goTools genomes
updated 3.4 years ago by • 0 • written 13.8 years ago by ★ 7.2k
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13
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How to plot NGS data?
GO BSgenome geneplotter PROcess BSgenome genomes GO BSgenome geneplotter PROcess genomes
updated 13.8 years ago by 25k • written 13.8 years ago by ▴ 30
0
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1
reply
914
views
MEDIPS R package reference genomes
genomes MEDIPS genomes MEDIPS
updated 13.9 years ago by ★ 6.8k • written 13.9 years ago by ▴ 220
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biomaRt access to ensemble genomes 11 fungi_mart_11
genomes genomes
updated 14.0 years ago by ▴ 60 • written 14.0 years ago by ★ 1.6k
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1
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1.0k
views
Addition of Orangutan genome to BSgenomes
Genetics BSgenome BSgenome genomes Genetics BSgenome BSgenome genomes
updated 14.1 years ago by ★ 6.8k • written 14.1 years ago by ▴ 10
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1
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1.2k
views
the procedure to annotate assembled transcriptom
annotate genomes annotate genomes
updated 14.1 years ago by 21k • written 14.1 years ago by ★ 2.0k
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1.6k
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Bioinformatics course - October 2011 Registration is now open
Microarray Cancer biomaRt ArrayExpress genomes SANTA Microarray Cancer biomaRt genomes
14.2 years ago Claude Chelala ▴ 40
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1.1k
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Conference announcement: Omics and Personalised Health, EMBL Heidelberg, 16-18 February 2012
genomes genomes
14.2 years ago Wolfgang Huber ★ 13k
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Postdoctoral positions at EMBL
Sequencing Genetics GO Network Cancer genomes Sequencing Genetics GO Network Cancer
14.2 years ago Wolfgang Huber ★ 13k
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IRanges: Request for a "step" argument in runsum
Coverage Annotation Cancer PROcess IRanges genomes Coverage Annotation Cancer PROcess
updated 14.4 years ago by 16k • written 14.5 years ago by ▴ 100
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1
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988
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IRanges: Request for a "step" argument in runsum
Cancer PROcess IRanges genomes Cancer PROcess IRanges genomes
updated 14.5 years ago by ★ 11k • written 14.5 years ago by 16k
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4
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IRanges: Request for a "step" argument in runsum
Cancer IRanges genomes Cancer IRanges genomes
updated 14.6 years ago by ★ 11k • written 14.6 years ago by ▴ 100
0
votes
8
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2.3k
views
Gene Lists and Genomes
GO genomes GO genomes
updated 14.6 years ago by ★ 4.2k • written 14.6 years ago by ▴ 240
0
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1.2k
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How do I use biomaRt to get upstreamFlank Genomic Sequence for many Genomes?
Alignment biomaRt genomes Alignment biomaRt genomes
15.0 years ago Noah Dowell ▴ 410
0
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1.2k
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how to go from an short read alignment file to a SNPs table for population genetic analysis
convert genomes convert genomes
15.0 years ago Sean Davis 21k
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1.4k
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how to go from an short read alignment file to a SNPs table for population genetic analysis
genomes genomes
updated 15.0 years ago by 21k • written 15.0 years ago by ▴ 290
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2
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1.9k
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a workflow of population genomic operations/analysis using bioconductor
Genetics genomes Genetics genomes
updated 15.0 years ago by ★ 11k • written 15.0 years ago by ▴ 290
0
votes
1
reply
987
views
Human genomic sequences
genomes genomes
updated 15.2 years ago by 6.7k • written 15.2 years ago by ▴ 30
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votes
2
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2.6k
views
E. coli annotation to map?
biomaRt genomes biomaRt genomes
updated 15.3 years ago by ▴ 500 • written 15.3 years ago by ▴ 40
0
votes
2
replies
2.2k
views
Bacterial genomics
Sequencing Microarray qPCR genomes Sequencing Microarray qPCR genomes
updated 15.3 years ago by 16k • written 15.3 years ago by ▴ 30
0
votes
2
replies
1.6k
views
error from rsamtools on 1000 genomes
Cancer HapMap Rsamtools genomes Cancer HapMap Rsamtools genomes
updated 15.4 years ago by 25k • written 15.4 years ago by ▴ 100
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votes
0
replies
1.1k
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ChIPpeakAnno Paper - Example Dataset not found
Transcription ChIPSeq Annotation chipseq genomes Transcription ChIPSeq Annotation chipseq
15.5 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
1.5k
views
Computational Biology Positions at EMBL (Heidelberg)
Sequencing Genetics genomes Sequencing Genetics genomes
15.8 years ago Wolfgang Huber ★ 13k
0
votes
0
replies
957
views
need output to contain probe x, y coordinates on array - AffyTiling
Microarray probe PROcess genomes Microarray probe PROcess genomes
16.0 years ago Charles Danko ▴ 40
115 results • Page 2 of 3
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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