Showing : Visualization • reset
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News: OmicCircos was updated
visualization omiccircos News
10.7 years ago Hu, Ying NIH/NCI [E] ▴ 50
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6
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3.4k
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Gviz::plotTracks for BiomartGeneRegionTrack() produces empty plots
gviz visualization
10.8 years ago Asta Laiho ▴ 120
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Interactive Visualization with Epivizr (what's new in this release)
epivizr visualization
11.1 years ago Hector Corrada Bravo ▴ 60
2
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2.4k
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ggbio: examples of overlaying multiple assay datasets
ggbio visualization ggbio
updated 11.2 years ago by ▴ 30 • written 11.2 years ago by ▴ 190
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Fwd: WGCNA: labeledHeatmap and verboseScatterplot correlations and p-values are not the same
Visualization Visualization
11.3 years ago Peter Langfelder ★ 3.0k
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Gviz: Plotting mean & CI for DataTrack
Annotation Visualization Gviz Annotation Visualization Gviz
11.3 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 11.3 years ago by 43k • written 11.3 years ago by ▴ 60
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ISMB talks: Pathview for pathway-based data integration and visualization
Pathways Visualization pathview Pathways Visualization pathview
11.4 years ago Luo Weijun ★ 1.6k
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Gviz: Plotting mean & CI for DataTrack
Annotation Visualization Gviz Annotation Visualization Gviz
11.5 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 11.7 years ago by ▴ 380 • written 11.7 years ago by 43k
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2
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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 11.8 years ago by 53k • written 11.8 years ago by ▴ 30
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2
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DESeq2 error
Visualization Clustering DESeq2 Visualization Clustering DESeq2
11.8 years ago Michael Love 43k
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Seattle Short Course, Feb 27-28: Introduction to Bioconductor for Sequence Analysis
RNASeq Visualization Cancer RNASeq Visualization Cancer
11.8 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
12.1 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
12.2 years ago • updated 12.1 years ago Luo Weijun ★ 1.6k
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3.1k
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Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
12.3 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
12.3 years ago Luo Weijun ★ 1.6k
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Pathview published in Bioinformatics
Visualization graph pathview Visualization graph pathview
12.3 years ago km ▴ 100
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1
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8.8k
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Using DESeq normalized gene count to replace FPKM?
Visualization DESeq Visualization DESeq
updated 12.3 years ago by ★ 3.8k • written 12.3 years ago by ▴ 10
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job advertisement
Genetics Alignment Visualization Genetics Alignment Visualization
12.4 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
12.4 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
12.4 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
12.4 years ago Martin Morgan 25k
0
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1
reply
1.3k
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status of visnab
Visualization ggbio Gviz Visualization ggbio Gviz
updated 12.5 years ago by ▴ 420 • written 12.5 years ago by ▴ 410
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Gviz: DataTrack heatmap
Visualization Gviz Visualization Gviz
12.6 years ago florian.hahne@novartis.com ★ 1.6k
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MA plots and assumptions
Normalization Visualization Normalization Visualization
updated 12.6 years ago by ★ 13k • written 12.6 years ago by ▴ 360
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5
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2.4k
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Question regarding cellhts2 output
Normalization Visualization PROcess cellHTS2 ASSIGN Normalization Visualization PROcess
12.6 years ago maziz@tgen.org ▴ 70
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Pathview package for pathway based data integration and visualization
Visualization pathview Visualization pathview
12.6 years ago Luo Weijun ★ 1.6k
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1.9k
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Bioconductor Digest, Vol 121, Issue 29
miRNA Annotation Normalization Visualization Clustering Infrastructure Cancer BSgenome vsn
12.7 years ago Matthew Thornton ▴ 390
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1.7k
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RPKM calculation genewise
Normalization Visualization easyRNASeq Normalization Visualization easyRNASeq
12.7 years ago delhomme@embl.de ★ 1.2k
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5
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Visualization of alignments with mismatch bases
SNP Coverage Alignment Visualization ggbio SNP Coverage Alignment Visualization ggbio
updated 12.7 years ago by ▴ 420 • written 12.7 years ago by ★ 11k
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Bioconductor Digest, Vol 120, Issue 12
Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy
12.8 years ago Matthew Thornton ▴ 390
0
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New course material: Intermediate R / Bioc for High-Throughput Sequence Analysis
Annotation Visualization Cancer Annotation Visualization Cancer
12.8 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
13.3 years ago Oliver Ruebenacker ▴ 110
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2012 Systems Bioinformatics Workshop
SAGE Visualization Network SAGE Visualization Network
13.4 years ago Christopher Bare ▴ 10
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1.5k
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Bioconductor 2.10 is released
Transcription Sequencing Microarray Annotation Normalization Visualization Network Bayesian
13.6 years ago Dan Tenenbaum ★ 8.2k
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4.1k
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Adjacency to network using R
Visualization Network convert Visualization Network convert
updated 13.7 years ago by ★ 4.2k • written 13.7 years ago by ▴ 120
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2.2k
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Gviz question
Visualization rtracklayer Gviz Visualization rtracklayer Gviz
13.7 years ago florian.hahne@novartis.com ★ 1.6k
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about GO analysis
GO Visualization GO Visualization
13.7 years ago Zhi Zhang ▴ 70
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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
13.8 years ago Florian Markowetz ▴ 20
0
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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
14.0 years ago Samuel Wuest ▴ 330
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1
reply
2.1k
views
DEseq for sample clustering
Visualization Clustering DESeq Visualization Clustering DESeq
updated 14.0 years ago by ★ 13k • written 14.0 years ago by ★ 13k
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0
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797
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R/Bioc workshops on Dec 8-12 at UC Riverside
Visualization Visualization
14.1 years ago Thomas Girke ★ 1.7k
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0
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1.5k
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Bioconductor 2.9 is released
Transcription Sequencing miRNA qPCR Proteomics Annotation Normalization Visualization cdf
14.1 years ago Dan Tenenbaum ★ 8.2k
0
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0
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1.4k
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
14.1 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
14.7 years ago Paolo Sonego ▴ 140
0
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1
reply
2.8k
views
Visualising the GO structure (RNA-seq) using topGO and goseq
Microarray GO Visualization Microarray GO Visualization
updated 14.7 years ago by ★ 7.2k • written 14.7 years ago by ▴ 140
0
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0
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2.3k
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Statistics and Bioinformatics Positions, Novartis Molecular Diagnostics, Cambridge MA USA and Basel, Switzerland
Visualization Visualization
15.0 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
15.2 years ago Eva Benito Garagorri ▴ 70
0
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0
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2.0k
views
GenomicFeatures makeTranscriptDbFromUCSC on refGene supported?
Visualization rtracklayer GenomicFeatures Visualization rtracklayer GenomicFeatures
15.4 years ago Erik van den Akker ▴ 50
156 results • Page 2 of 4
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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