Showing : visualization • reset
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1000 R tutorials/Links
Sequencing Microarray Genetics Visualization Network Bayesian Classification Clustering
13.9 years ago David Lyon ▴ 340
0
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8
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12k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2 pvalue visualization enhancedvolcano rnaseq
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
0
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4
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8.9k
views
Agilent 2-color Microarray data analysis tutorial
Microarray Visualization Clustering Microarray Visualization Clustering
updated 14.3 years ago by 25k • written 14.3 years ago by ▴ 140
8
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12
replies
8.6k
views
EdgeR: Explaning dispersion types to newbies
edger dispersion estimatedispersions visualization teaching
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 20
0
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1
reply
8.3k
views
Using DESeq normalized gene count to replace FPKM?
Visualization DESeq Visualization DESeq
updated 10.7 years ago by ★ 3.7k • written 10.7 years ago by ▴ 10
11
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0
replies
5.8k
views
Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
8.8 years ago Martin Morgan 25k
0
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0
replies
5.1k
views
Reading GFF files into R and GenomeGraphs
Coverage Annotation Visualization convert GLAD GenomeGraphs rtracklayer IRanges Coverage
14.7 years ago Michael Dondrup ▴ 140
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7
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4.9k
views
Visualization of rownames in the heatmap.2 function for selected DE genes of a microarray dataset
heatmap.2 gplots differential gene expression visualization
9.1 years ago svlachavas ▴ 830
2
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2
replies
4.2k
views
How can I visualize Gene Set Enrichment Results from gseGo fun. (clusterProfiler)?
ggplot2 clusterprofiler visualization gseGo
7.0 years ago • updated 3.4 years ago tcalvo ▴ 90
7
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0
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3.7k
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Tutorial: New edX "Data analysis for Life Sciences" module: High performance computing for reproducible genomics
annotation genomicranges visualization docker shiny Tutorial
8.1 years ago Vincent J. Carey, Jr. 6.7k
8
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0
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3.6k
views
Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
8.8 years ago Martin Morgan 25k
2
votes
1
reply
3.5k
views
Heatmap function
Visualization Visualization
updated 20.5 years ago by ▴ 210 • written 20.5 years ago by ▴ 150
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5
replies
3.5k
views
Adjacency to network using R
Visualization Network convert Visualization Network convert
updated 12.1 years ago by ★ 4.2k • written 12.1 years ago by ▴ 120
0
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2
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3.4k
views
Mapping gene IDs to gene symbol of KEGG pathways with "Pathview"
Pathview KEGG annotation gene symbol visualization
updated 8.8 years ago by ★ 1.6k • written 8.8 years ago by ▴ 130
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6
replies
3.3k
views
Fwd: WGCNA: labeledHeatmap and verboseScatterplot correlations and p-values are not the same
Visualization Visualization
9.7 years ago Peter Langfelder ★ 3.0k
0
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0
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3.2k
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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
10.7 years ago Luo Weijun ★ 1.6k
0
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1
reply
3.0k
views
GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
GO Visualization edgeR gage GO Visualization edgeR gage
10.6 years ago Luo Weijun ★ 1.6k
0
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6
replies
2.9k
views
Gviz::plotTracks for BiomartGeneRegionTrack() produces empty plots
gviz visualization
9.3 years ago • updated 9.2 years ago Asta Laiho ▴ 120
5
votes
11
replies
2.9k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 10 months ago by ▴ 20
1
vote
2
replies
2.7k
views
gene expression visualization: lineplot with ggplot2
ggplot2 lineplot visualization
updated 8.9 years ago by ▴ 180 • written 8.9 years ago by ▴ 130
0
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0
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2.6k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
10.7 years ago Luo Weijun ★ 1.6k
0
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5
replies
2.6k
views
Gene Symbol with Pathview
pathview bioconductor kegg visualization
updated 8.5 years ago by ★ 1.6k • written 8.5 years ago by • 0
0
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2
replies
2.6k
views
DESeq2 error
Visualization Clustering DESeq2 Visualization Clustering DESeq2
10.2 years ago Michael Love 41k
0
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2
replies
2.5k
views
Questions about multi-factor contrast setting in DESeq2
GO Visualization Clustering limma edgeR DESeq2 GO Visualization Clustering limma edgeR
updated 10.1 years ago by ▴ 380 • written 10.1 years ago by 41k
0
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1
reply
2.4k
views
Visualising the GO structure (RNA-seq) using topGO and goseq
Microarray GO Visualization Microarray GO Visualization
updated 13.1 years ago by ★ 7.2k • written 13.1 years ago by ▴ 140
1
vote
1
reply
2.3k
views
Using DESeq2: experimental design and extracting results
Visualization DESeq DESeq2 Visualization DESeq DESeq2
updated 9.7 years ago by 41k • written 9.7 years ago by ▴ 60
3
votes
5
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2.3k
views
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
pathview clusterProfiler KEGGpath visualization Graphviz
updated 8.4 years ago by ★ 1.6k • written 8.4 years ago by ▴ 830
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3
replies
2.2k
views
RNAseq read coverage plot: What tool?
rnaseq visualization plotcoveragehist
updated 7.0 years ago by ★ 1.3k • written 7.0 years ago by ▴ 130
0
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7
replies
2.2k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 7.6 years ago by • 0 • written 14.0 years ago by ★ 1.6k
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1
reply
2.2k
views
Bioconductor Digest, Vol 120, Issue 12
Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy
11.2 years ago Matthew Thornton ▴ 350
0
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0
replies
2.1k
views
Visualising the GO structure (RNA-seq) using topGO, and goseq
Microarray GO Visualization graph topGO goseq Microarray GO Visualization graph topGO
13.1 years ago Paolo Sonego ▴ 140
0
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2
replies
2.1k
views
What RNA-Seq expression estimates to use for plotting to show voom/limma Differential expression
Visualization graph limma Visualization graph limma
updated 10.2 years ago by 50k • written 10.2 years ago by ▴ 30
2
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1
reply
2.1k
views
ggbio: examples of overlaying multiple assay datasets
ggbio visualization ggbio
updated 9.6 years ago by ▴ 30 • written 9.6 years ago by ▴ 190
0
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0
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2.0k
views
Statistics and Bioinformatics Positions, Novartis Molecular Diagnostics, Cambridge MA USA and Basel, Switzerland
Visualization Visualization
13.4 years ago A.J. Rossini ▴ 210
0
votes
1
reply
1.9k
views
Entrez Gene ID to Probe Set Name
aCGH Sequencing miRNA Microarray Annotation Normalization GO Preprocessing Visualization
updated 15.5 years ago by ★ 7.2k • written 15.5 years ago by ▴ 300
0
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0
replies
1.9k
views
Gviz: DataTrack heatmap
Visualization Gviz Visualization Gviz
11.0 years ago florian.hahne@novartis.com ★ 1.6k
0
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0
replies
1.9k
views
Gviz question
Visualization rtracklayer Gviz Visualization rtracklayer Gviz
12.1 years ago florian.hahne@novartis.com ★ 1.6k
1
vote
3
replies
1.9k
views
Visualizing gene counts and variance stabilization
deseq2 rnaseq variancestabilizingtransformation visualization
updated 8.8 years ago by 41k • written 8.8 years ago by ▴ 40
0
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5
replies
1.9k
views
Question regarding cellhts2 output
Normalization Visualization PROcess cellHTS2 ASSIGN Normalization Visualization PROcess
11.0 years ago maziz@tgen.org ▴ 70
1
vote
0
replies
1.9k
views
Job: PhD position - Heidelberg: Bioinformatic analysis of high-throughput and image-based RNAi screening data
high-throughput screening RNAi image analysis data integration visualization Job
9.1 years ago e.schmidt ▴ 10
0
votes
9
replies
1.9k
views
visualizing alignment without realignment
msa alignment visualization
updated 5.1 years ago by 25k • written 5.1 years ago by • 0
0
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0
replies
1.8k
views
qPCR Events and 30% Discount on qPCR workshops
miRNA qPCR Epigenetics GO Visualization Network probe microRNA miRNA qPCR Epigenetics
14.5 years ago qPCR Platform - the reference in real-t… ▴ 170
0
votes
1
reply
1.8k
views
DEseq for sample clustering
Visualization Clustering DESeq Visualization Clustering DESeq
updated 12.4 years ago by ★ 13k • written 12.4 years ago by ★ 13k
0
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0
replies
1.8k
views
Job: Post-Doctoral Research Fellow - Patient Genomics Data Visualization
visualization genomics personalized medicine systemsbiology js Job
9.0 years ago Hamid Bolouri ▴ 50
0
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0
replies
1.7k
views
heatmap and Hierarchical Clustering from limma results
Visualization limma Visualization limma
16.0 years ago Abhilash Venu ▴ 340
1
vote
0
replies
1.7k
views
Pathview and GAGE now work with essentially all KEGG species
Visualization gage pathview Visualization gage pathview
10.5 years ago Luo Weijun ★ 1.6k
0
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0
replies
1.7k
views
GenomicFeatures makeTranscriptDbFromUCSC on refGene supported?
Visualization rtracklayer GenomicFeatures Visualization rtracklayer GenomicFeatures
13.8 years ago Erik van den Akker ▴ 50
3
votes
0
replies
1.7k
views
News: BioCAsia, 8 Sept 2015, Tokyo
sequencing transcription epigenomics visualization infrastructure News
8.8 years ago • updated 8.7 years ago Matthew Ritchie ▴ 1000
1
vote
3
replies
1.7k
views
copy number variation analysis (CNV)
copynumber plot visualization NGS gene
updated 3.4 years ago by ▴ 190 • written 3.5 years ago by • 0
0
votes
2
replies
1.6k
views
Visualizing GOstats HyperGTest results
GO Visualization GOstats GO Visualization GOstats
updated 16.2 years ago by 65k • written 16.3 years ago by ▴ 600
50 results • Page 1 of 1
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Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by sredemption • 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…
Votes
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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