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Visualization
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0
votes
6
replies
2.9k
views
Gviz::plotTracks for BiomartGeneRegionTrack() produces empty plots
gviz
visualization
9.2 years ago
Asta Laiho
▴ 120
0
votes
4
replies
1.3k
views
Pathview published in Bioinformatics
Visualization
pathview
Visualization
pathview
10.8 years ago
Luo Weijun
★ 1.6k
0
votes
5
replies
2.6k
views
Gene Symbol with Pathview
pathview
bioconductor
kegg
visualization
updated 8.4 years ago by
Luo Weijun
★ 1.6k • written 8.5 years ago by
abhinavbn
• 0
0
votes
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
0
votes
6
replies
3.3k
views
Fwd: WGCNA: labeledHeatmap and verboseScatterplot correlations and p-values are not the same
Visualization
Visualization
9.6 years ago
Peter Langfelder
★ 2.9k
0
votes
2
replies
888
views
ANN: Bioconductor short course June 1-3 in Seattle
Preprocessing
Visualization
Cancer
Preprocessing
Visualization
Cancer
19.0 years ago
Seth Falcon
★ 7.4k
4
votes
6
replies
1.3k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
22 months ago
mohammedtoufiq91
▴ 10
0
votes
4
replies
1.3k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer
Visualization
updated 2.4 years ago by
Hervé Pagès
16k • written 2.4 years ago by
chase.mateusiak
• 0
3
votes
5
replies
2.2k
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
Luo Weijun
★ 1.6k • written 8.4 years ago by
svlachavas
▴ 830
0
votes
7
replies
2.2k
views
Bioconductor 2.6 is released
Sequencing
Microarray
Visualization
Infrastructure
PROcess
beadarray
keggorthology
eisa
updated 7.6 years ago by
wangyizhusss
• 0 • written 13.9 years ago by
Patrick Aboyoun
★ 1.6k
0
votes
2
replies
2.6k
views
DESeq2 error
Visualization
Clustering
DESeq2
Visualization
Clustering
DESeq2
10.1 years ago
Michael Love
41k
0
votes
2
replies
1.3k
views
proposed: a bridge between R and Cytoscape
Visualization
Network
graph
Visualization
Network
graph
updated 13.8 years ago by
Steve Lianoglou
★ 13k • written 13.8 years ago by
Paul Shannon
★ 1.1k
2
votes
4
replies
1.6k
views
chimeraviz - import own fusion file for visualization
visualization
chimeraviz
updated 2.7 years ago by
Iman
• 0 • written 6.7 years ago by
verena.tischler
▴ 10
0
votes
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 10.1 years ago by
Gordon Smyth
50k • written 10.1 years ago by
Heather Estrella
▴ 30
0
votes
3
replies
2.2k
views
RNAseq read coverage plot: What tool?
rnaseq
visualization
plotcoveragehist
updated 6.9 years ago by
Ou, Jianhong
★ 1.3k • written 6.9 years ago by
alakatos
▴ 130
0
votes
2
replies
1.4k
views
DMRcate DMR.plot Turn Off Group Means
dmrcate
visualization
updated 7.2 years ago by
Tim Peters
▴ 160 • written 7.2 years ago by
csugai
• 0
0
votes
1
reply
1.2k
views
Survey on interactive visualization and Bioconductor
visualization
epivizr
7.8 years ago
Hector Corrada Bravo
▴ 60
2
votes
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
1
vote
3
replies
1.9k
views
Visualizing gene counts and variance stabilization
deseq2
rnaseq
variancestabilizingtransformation
visualization
updated 8.8 years ago by
Michael Love
41k • written 8.8 years ago by
ysdel
▴ 40
0
votes
1
reply
1.0k
views
status of visnab
Visualization
ggbio
Gviz
Visualization
ggbio
Gviz
updated 10.9 years ago by
Tengfei Yin
▴ 420 • written 10.9 years ago by
Abhishek Pratap
▴ 410
1
vote
1
reply
1.4k
views
Visualizing Structural variants
visualization
SV
updated 8.9 years ago by
Vincent J. Carey, Jr.
6.7k • written 8.9 years ago by
Abhishek Pratap
▴ 190
1
vote
2
replies
2.7k
views
gene expression visualization: lineplot with ggplot2
ggplot2
lineplot
visualization
updated 8.8 years ago by
Jeremy Ng
▴ 180 • written 8.8 years ago by
alakatos
▴ 130
0
votes
1
reply
1.9k
views
Entrez Gene ID to Probe Set Name
aCGH
Sequencing
miRNA
Microarray
Annotation
Normalization
GO
Preprocessing
Visualization
updated 15.4 years ago by
Marc Carlson
★ 7.2k • written 15.4 years ago by
McGee, Monnie
▴ 300
2
votes
2
replies
1.1k
views
What can be done to separate the healthy and patient samples in PCA plot and Distance matrix
deseq2
PCAplot
Visualization
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
Mithil Gaikwad
• 0
0
votes
2
replies
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
Luo Weijun
★ 1.6k • written 8.8 years ago by
alakatos
▴ 130
0
votes
1
reply
697
views
comparative genomics
Visualization
Visualization
updated 18.8 years ago by
Sean Davis
21k • written 18.8 years ago by
Sorani, Marco
▴ 30
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
Michael Love
41k • written 9.7 years ago by
bio2001
▴ 60
0
votes
1
reply
1.0k
views
Several questions goCluster and GOstats...
Annotation
GO
Visualization
Yeast
goCluster
Annotation
GO
Visualization
Yeast
goCluster
updated 18.6 years ago by
Gunnar Wrobel
▴ 60 • written 18.6 years ago by
Lourdes Peña Castillo
▴ 140
2
votes
1
reply
3.5k
views
Heatmap function
Visualization
Visualization
updated 20.4 years ago by
Furge, Kyle
▴ 210 • written 20.4 years ago by
Marcus
▴ 150
0
votes
1
reply
1.4k
views
ChIPseeker gene body plot
chipseeker
visualization
updated 7.8 years ago by
Guangchuang Yu
★ 1.2k • written 7.8 years ago by
igor
▴ 40
2
votes
1
reply
2.0k
views
ggbio: examples of overlaying multiple assay datasets
ggbio
visualization
ggbio
updated 9.5 years ago by
Panagiotis Moulos
▴ 30 • written 9.5 years ago by
Abhishek Pratap
▴ 190
0
votes
1
reply
3.0k
views
GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
GO
Visualization
edgeR
gage
GO
Visualization
edgeR
gage
10.5 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
690
views
MA plots and assumptions
Normalization
Visualization
Normalization
Visualization
updated 10.9 years ago by
Wolfgang Huber
★ 13k • written 10.9 years ago by
Juliet Hannah
▴ 360
0
votes
1
reply
8.2k
views
Using DESeq normalized gene count to replace FPKM?
Visualization
DESeq
Visualization
DESeq
updated 10.7 years ago by
Simon Anders
★ 3.7k • written 10.7 years ago by
Jike Cui
▴ 10
0
votes
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
Ming
▴ 380 • written 10.1 years ago by
Michael Love
41k
0
votes
2
replies
1.6k
views
Visualizing GOstats HyperGTest results
GO
Visualization
GOstats
GO
Visualization
GOstats
updated 16.2 years ago by
James W. MacDonald
65k • written 16.2 years ago by
Srinivas Iyyer
▴ 600
0
votes
1
reply
1.8k
views
DEseq for sample clustering
Visualization
Clustering
DESeq
Visualization
Clustering
DESeq
updated 12.4 years ago by
Wolfgang Huber
★ 13k • written 12.4 years ago by
Guest User
★ 13k
0
votes
5
replies
3.4k
views
Adjacency to network using R
Visualization
Network
convert
Visualization
Network
convert
updated 12.0 years ago by
Tim Triche
★ 4.2k • written 12.0 years ago by
pankaj borah
▴ 120
0
votes
5
replies
1.6k
views
Visualization of alignments with mismatch bases
SNP
Coverage
Alignment
Visualization
ggbio
SNP
Coverage
Alignment
Visualization
ggbio
updated 11.1 years ago by
Tengfei Yin
▴ 420 • written 11.1 years ago by
Michael Lawrence
★ 11k
0
votes
1
reply
768
views
cosmo package - Tk requirement?
Visualization
cosmo
Visualization
cosmo
updated 17.2 years ago by
Oliver Bembom
▴ 30 • written 17.2 years ago by
Diggans, James C.
▴ 10
0
votes
1
reply
2.4k
views
Visualising the GO structure (RNA-seq) using topGO and goseq
Microarray
GO
Visualization
Microarray
GO
Visualization
updated 13.0 years ago by
Marc Carlson
★ 7.2k • written 13.0 years ago by
Paolo Sonego
▴ 140
0
votes
1
reply
2.2k
views
Bioconductor Digest, Vol 120, Issue 12
Microarray
qPCR
Coverage
Annotation
Pathways
Visualization
Cancer
Breast
Organism
affy
11.1 years ago
Matthew Thornton
▴ 350
0
votes
1
reply
831
views
Visualization of multiple alignments in bioconductor
Genetics
Visualization
Genetics
Visualization
updated 15.7 years ago by
Martin Morgan
25k • written 15.7 years ago by
Schraga Schwartz
▴ 10
0
votes
1
reply
1.1k
views
Color in the lefs of a dendrogram?
Visualization
Clustering
Visualization
Clustering
updated 19.4 years ago by
Martin Maechler
▴ 330 • written 19.4 years ago by
Johan Lindberg
▴ 270
0
votes
4
replies
8.8k
views
Agilent 2-color Microarray data analysis tutorial
Microarray
Visualization
Clustering
Microarray
Visualization
Clustering
updated 14.2 years ago by
Martin Morgan
25k • written 14.2 years ago by
Chuming Chen
▴ 140
0
votes
3
replies
1.5k
views
Bioconductor 2.3 is released
aCGH
Sequencing
miRNA
Microarray
Visualization
Bayesian
Classification
Survival
Yeast
LPE
15.4 years ago
Patrick Aboyoun
★ 1.6k
0
votes
1
reply
1.4k
views
2 Courses Near You - (1) Introduction to R/S+ programming: Microarrays Analysis and Bioconductor, (2) R/Splus Fundamentals and Programming Techniques
Visualization
Clustering
Visualization
Clustering
updated 17.8 years ago by
Francois Collin
▴ 130 • written 17.8 years ago by
sue@xlsolutions-corp.com
▴ 570
0
votes
2
replies
1.5k
views
FlowViz graphics problems
Microarray
Visualization
graph
flowCore
flowViz
Microarray
Visualization
graph
flowCore
updated 14.8 years ago by
Nishant Gopalakrishnan
▴ 340 • written 14.8 years ago by
Anja Schiel
▴ 20
0
votes
1
reply
1.3k
views
Talk & Poster - Final Call - qPCR 2009 Event
SNP
qPCR
Normalization
Visualization
Regression
Cancer
probe
PROcess
microRNA
SNP
qPCR
15.3 years ago
qPCR Platform - the reference in real-t…
▴ 170
0
votes
1
reply
1.1k
views
LIMMA, SAM & clustering
Visualization
Clustering
limma
Visualization
Clustering
limma
updated 18.2 years ago by
James W. MacDonald
65k • written 18.2 years ago by
daniela.marconi@libero.it
▴ 100
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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