Showing : Visualization • reset
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News: OmicCircos was updated
visualization omiccircos News
10.9 years ago Hu, Ying NIH/NCI [E] ▴ 50
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6
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3.5k
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Gviz::plotTracks for BiomartGeneRegionTrack() produces empty plots
gviz visualization
11.0 years ago Asta Laiho ▴ 120
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Interactive Visualization with Epivizr (what's new in this release)
epivizr visualization
11.2 years ago Hector Corrada Bravo ▴ 60
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1
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2.4k
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ggbio: examples of overlaying multiple assay datasets
ggbio visualization ggbio
updated 11.3 years ago by ▴ 30 • written 11.4 years ago by ▴ 190
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Fwd: WGCNA: labeledHeatmap and verboseScatterplot correlations and p-values are not the same
Visualization Visualization
11.5 years ago Peter Langfelder ★ 3.0k
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Gviz: Plotting mean & CI for DataTrack
Annotation Visualization Gviz Annotation Visualization Gviz
11.5 years ago florian.hahne@novartis.com ★ 1.6k
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Using DESeq2: experimental design and extracting results
Visualization DESeq DESeq2 Visualization DESeq DESeq2
updated 11.5 years ago by 43k • written 11.5 years ago by ▴ 60
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ISMB talks: Pathview for pathway-based data integration and visualization
Pathways Visualization pathview Pathways Visualization pathview
11.5 years ago Luo Weijun ★ 1.6k
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Gviz: Plotting mean & CI for DataTrack
Annotation Visualization Gviz Annotation Visualization Gviz
11.6 years ago Shraddha Pai ▴ 80
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Questions about multi-factor contrast setting in DESeq2
GO Visualization Clustering limma edgeR DESeq2 GO Visualization Clustering limma edgeR
updated 11.9 years ago by ▴ 380 • written 11.9 years ago by 43k
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What RNA-Seq expression estimates to use for plotting to show voom/limma Differential expression
Visualization graph limma Visualization graph limma
updated 12.0 years ago by 53k • written 12.0 years ago by ▴ 30
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2
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DESeq2 error
Visualization Clustering DESeq2 Visualization Clustering DESeq2
12.0 years ago Michael Love 43k
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1.3k
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Seattle Short Course, Feb 27-28: Introduction to Bioconductor for Sequence Analysis
RNASeq Visualization Cancer RNASeq Visualization Cancer
12.0 years ago Martin Morgan 25k
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Pathview and GAGE now work with essentially all KEGG species
Visualization gage pathview Visualization gage pathview
12.3 years ago Luo Weijun ★ 1.6k
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1
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GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
GO Visualization edgeR gage GO Visualization edgeR gage
12.3 years ago Luo Weijun ★ 1.6k
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3.2k
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Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
12.5 years ago Luo Weijun ★ 1.6k
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Pathview+GAGE workflow on RNA-seq data pathway analysis and visualization (was: Pathview published in Bioinformatics)
Annotation Pathways Visualization graph PROcess gage pathview Annotation Pathways graph
12.5 years ago Luo Weijun ★ 1.6k
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Pathview published in Bioinformatics
Visualization graph pathview Visualization graph pathview
12.5 years ago km ▴ 100
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8.8k
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Using DESeq normalized gene count to replace FPKM?
Visualization DESeq Visualization DESeq
updated 12.5 years ago by ★ 3.8k • written 12.5 years ago by ▴ 10
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job advertisement
Genetics Alignment Visualization Genetics Alignment Visualization
12.5 years ago Zhenyu Xu ▴ 10
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BioC 2013, July 17 (Developer Day) 18-19: 'Early' registration deadline July 1
Cheminformatics Visualization Cancer Ovarian DEXSeq minfi DESeq2 BaseSpaceR epivizr minfi
12.6 years ago Martin Morgan 25k
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4
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1.8k
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Pathview published in Bioinformatics
Visualization pathview Visualization pathview
12.6 years ago Luo Weijun ★ 1.6k
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0
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1.3k
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BioC 2013: Talks and Workshops
Visualization Cancer Ovarian DEXSeq DESeq2 BaseSpaceR Visualization Cancer Ovarian DEXSeq
12.6 years ago Martin Morgan 25k
0
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1
reply
1.4k
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status of visnab
Visualization ggbio Gviz Visualization ggbio Gviz
updated 12.7 years ago by ▴ 420 • written 12.7 years ago by ▴ 410
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Gviz: DataTrack heatmap
Visualization Gviz Visualization Gviz
12.7 years ago florian.hahne@novartis.com ★ 1.6k
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MA plots and assumptions
Normalization Visualization Normalization Visualization
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ▴ 360
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5
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2.5k
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Question regarding cellhts2 output
Normalization Visualization PROcess cellHTS2 ASSIGN Normalization Visualization PROcess
12.8 years ago maziz@tgen.org ▴ 70
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1.3k
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Pathview package for pathway based data integration and visualization
Visualization pathview Visualization pathview
12.8 years ago Luo Weijun ★ 1.6k
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Bioconductor Digest, Vol 121, Issue 29
miRNA Annotation Normalization Visualization Clustering Infrastructure Cancer BSgenome vsn
12.8 years ago Matthew Thornton ▴ 390
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RPKM calculation genewise
Normalization Visualization easyRNASeq Normalization Visualization easyRNASeq
12.9 years ago delhomme@embl.de ★ 1.2k
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Visualization of alignments with mismatch bases
SNP Coverage Alignment Visualization ggbio SNP Coverage Alignment Visualization ggbio
updated 12.9 years ago by ▴ 420 • written 12.9 years ago by ★ 11k
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Bioconductor Digest, Vol 120, Issue 12
Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy
12.9 years ago Matthew Thornton ▴ 390
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New course material: Intermediate R / Bioc for High-Throughput Sequence Analysis
Annotation Visualization Cancer Annotation Visualization Cancer
12.9 years ago Martin Morgan 25k
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1.1k
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BioPAX parsing
Pathways Visualization Network graph Pathways Visualization Network graph
13.5 years ago Oliver Ruebenacker ▴ 110
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2012 Systems Bioinformatics Workshop
SAGE Visualization Network SAGE Visualization Network
13.6 years ago Christopher Bare ▴ 10
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1.6k
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Bioconductor 2.10 is released
Transcription Sequencing Microarray Annotation Normalization Visualization Network Bayesian
13.8 years ago Dan Tenenbaum ★ 8.2k
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Adjacency to network using R
Visualization Network convert Visualization Network convert
updated 13.8 years ago by ★ 4.2k • written 13.8 years ago by ▴ 120
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Gviz question
Visualization rtracklayer Gviz Visualization rtracklayer Gviz
13.9 years ago florian.hahne@novartis.com ★ 1.6k
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about GO analysis
GO Visualization GO Visualization
13.9 years ago Zhi Zhang ▴ 70
0
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0
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1.7k
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Open Position :: Postdoc in systems genetics in Cambridge
Transcription Genetics Visualization Network Cancer Breast Lung Transcription Genetics
14.0 years ago Florian Markowetz ▴ 20
0
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1.5k
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GenomeGraphs plots: polygon tracks for sequencing coverage data
Sequencing Coverage Visualization GenomeGraphs Sequencing Coverage Visualization
14.1 years ago Samuel Wuest ▴ 330
0
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1
reply
2.1k
views
DEseq for sample clustering
Visualization Clustering DESeq Visualization Clustering DESeq
updated 14.2 years ago by ★ 13k • written 14.2 years ago by ★ 13k
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0
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822
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R/Bioc workshops on Dec 8-12 at UC Riverside
Visualization Visualization
14.2 years ago Thomas Girke ★ 1.7k
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1.5k
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Bioconductor 2.9 is released
Transcription Sequencing miRNA qPCR Proteomics Annotation Normalization Visualization cdf
14.2 years ago Dan Tenenbaum ★ 8.2k
0
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0
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1.5k
views
topGO graph visualization functions crashing under R 2.13.2 with Graphviz 2.20.3.1
GO Visualization graph Rgraphviz topGO GO Visualization graph Rgraphviz topGO
14.3 years ago Joseph Skaf ▴ 20
0
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0
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2.4k
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Visualising the GO structure (RNA-seq) using topGO, and goseq
Microarray GO Visualization graph topGO goseq Microarray GO Visualization graph topGO
14.8 years ago Paolo Sonego ▴ 140
0
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1
reply
2.9k
views
Visualising the GO structure (RNA-seq) using topGO and goseq
Microarray GO Visualization Microarray GO Visualization
updated 14.8 years ago by ★ 7.2k • written 14.8 years ago by ▴ 140
0
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0
replies
2.4k
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Statistics and Bioinformatics Positions, Novartis Molecular Diagnostics, Cambridge MA USA and Basel, Switzerland
Visualization Visualization
15.1 years ago A.J. Rossini ▴ 210
0
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0
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1.4k
views
BioNet - interpretation of node score
Microarray Visualization Network BioNet Microarray Visualization Network BioNet
15.4 years ago Eva Benito Garagorri ▴ 70
0
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0
replies
2.0k
views
GenomicFeatures makeTranscriptDbFromUCSC on refGene supported?
Visualization rtracklayer GenomicFeatures Visualization rtracklayer GenomicFeatures
15.5 years ago Erik van den Akker ▴ 50
156 results • Page 2 of 4
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Replies
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You may want to speak with a local statistician, because you don't just want to find the first full rank matrix and run with that if it doe…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
It is fine for your mass spec facility to include blank samples as part of their internal QC, but such samples should not in my opinion be …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Hm, okay, in building a fake model by hand I think I'm realizing the problem: `mouse` and its variants are ideally acting as basically a ra…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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