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Visualization
•
reset
8
votes
12
replies
8.8k
views
EdgeR: Explaning dispersion types to newbies
edger
dispersion
estimatedispersions
visualization
teaching
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
Mr.RB
▴ 20
5
votes
11
replies
3.1k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
5
votes
11
replies
1.5k
views
Visualization tool for GC-bias in SE data?
GC-bias
ALPINE
visualization
updated 3.9 years ago by
Michael Love
42k • written 3.9 years ago by
AKSR
▴ 20
0
votes
9
replies
1.9k
views
visualizing alignment without realignment
msa
alignment
visualization
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
tim.ivanov.92
• 0
0
votes
8
replies
12k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2
pvalue
visualization
enhancedvolcano
rnaseq
updated 5.3 years ago by
Michael Love
42k • written 5.3 years ago by
ricardo3889
• 0
0
votes
7
replies
2.3k
views
Bioconductor 2.6 is released
Sequencing
Microarray
Visualization
Infrastructure
PROcess
beadarray
keggorthology
eisa
updated 7.7 years ago by
wangyizhusss
• 0 • written 14.1 years ago by
Patrick Aboyoun
★ 1.6k
0
votes
7
replies
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
0
votes
6
replies
3.4k
views
Fwd: WGCNA: labeledHeatmap and verboseScatterplot correlations and p-values are not the same
Visualization
Visualization
9.8 years ago
Peter Langfelder
★ 3.0k
4
votes
6
replies
1.4k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
24 months ago
mohammedtoufiq91
▴ 10
0
votes
6
replies
2.9k
views
Gviz::plotTracks for BiomartGeneRegionTrack() produces empty plots
gviz
visualization
9.3 years ago
Asta Laiho
▴ 120
3
votes
5
replies
2.3k
views
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
pathview
clusterProfiler
KEGGpath
visualization
Graphviz
updated 8.5 years ago by
Luo Weijun
★ 1.6k • written 8.5 years ago by
svlachavas
▴ 830
0
votes
5
replies
2.7k
views
Gene Symbol with Pathview
pathview
bioconductor
kegg
visualization
updated 8.6 years ago by
Luo Weijun
★ 1.6k • written 8.6 years ago by
abhinavbn
• 0
0
votes
5
replies
1.6k
views
Visualization of alignments with mismatch bases
SNP
Coverage
Alignment
Visualization
ggbio
SNP
Coverage
Alignment
Visualization
ggbio
updated 11.2 years ago by
Tengfei Yin
▴ 420 • written 11.2 years ago by
Michael Lawrence
★ 11k
0
votes
5
replies
3.5k
views
Adjacency to network using R
Visualization
Network
convert
Visualization
Network
convert
updated 12.1 years ago by
Tim Triche
★ 4.2k • written 12.1 years ago by
pankaj borah
▴ 120
0
votes
5
replies
1.9k
views
Question regarding cellhts2 output
Normalization
Visualization
PROcess
cellHTS2
ASSIGN
Normalization
Visualization
PROcess
11.1 years ago
maziz@tgen.org
▴ 70
0
votes
5
replies
1.6k
views
BED15 format for rtracklayer
Microarray
Visualization
rtracklayer
Microarray
Visualization
rtracklayer
updated 14.8 years ago by
Michael Lawrence
▴ 620 • written 14.8 years ago by
rcaloger
▴ 500
0
votes
4
replies
1.3k
views
Pathview published in Bioinformatics
Visualization
pathview
Visualization
pathview
10.9 years ago
Luo Weijun
★ 1.6k
0
votes
4
replies
1.4k
views
Deseq2 problem visualizing gene expression with batch corrected values
deseq2
limma
differential expression
visualization
updated 5.9 years ago by
Michael Love
42k • written 5.9 years ago by
Mbosio85
• 0
2
votes
4
replies
1.6k
views
chimeraviz - import own fusion file for visualization
visualization
chimeraviz
updated 2.8 years ago by
Iman
• 0 • written 6.9 years ago by
verena.tischler
▴ 10
0
votes
4
replies
8.9k
views
Agilent 2-color Microarray data analysis tutorial
Microarray
Visualization
Clustering
Microarray
Visualization
Clustering
updated 14.3 years ago by
Martin Morgan
25k • written 14.3 years ago by
Chuming Chen
▴ 140
0
votes
4
replies
1.4k
views
rtracklayer can't access hg38 on UCSC?
rtracklayer
Visualization
updated 2.5 years ago by
Hervé Pagès
16k • written 2.5 years ago by
chase.mateusiak
• 0
0
votes
3
replies
1.6k
views
Bioconductor 2.3 is released
aCGH
Sequencing
miRNA
Microarray
Visualization
Bayesian
Classification
Survival
Yeast
LPE
15.6 years ago • updated 15.5 years ago
Patrick Aboyoun
★ 1.6k
1
vote
3
replies
1.9k
views
Visualizing gene counts and variance stabilization
deseq2
rnaseq
variancestabilizingtransformation
visualization
updated 8.9 years ago by
Michael Love
42k • written 8.9 years ago by
ysdel
▴ 40
1
vote
3
replies
1.7k
views
copy number variation analysis (CNV)
copynumber
plot
visualization
NGS
gene
updated 3.4 years ago by
Ram
▴ 210 • written 3.6 years ago by
sijing.gsj
• 0
0
votes
3
replies
2.3k
views
RNAseq read coverage plot: What tool?
rnaseq
visualization
plotcoveragehist
updated 7.1 years ago by
Ou, Jianhong
★ 1.3k • written 7.1 years ago by
alakatos
▴ 130
3
votes
3
replies
1.1k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger
clustering
visualization
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
thindmarsmission
▴ 10
0
votes
2
replies
1.4k
views
DMRcate DMR.plot Turn Off Group Means
dmrcate
visualization
updated 7.3 years ago by
Tim Peters
▴ 180 • written 7.3 years ago by
csugai
• 0
0
votes
2
replies
337
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 8 weeks ago by
Michael Love
42k • written 8 weeks ago by
gglatzer
• 0
0
votes
2
replies
3.5k
views
Mapping gene IDs to gene symbol of KEGG pathways with "Pathview"
Pathview
KEGG
annotation
gene symbol
visualization
updated 8.9 years ago by
Luo Weijun
★ 1.6k • written 8.9 years ago by
alakatos
▴ 130
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 5.3 years ago by
Michael Love
42k • written 5.3 years ago by
Mithil Gaikwad
• 0
2
votes
2
replies
4.3k
views
How can I visualize Gene Set Enrichment Results from gseGo fun. (clusterProfiler)?
ggplot2
clusterprofiler
visualization
gseGo
7.1 years ago • updated 3.5 years ago
tcalvo
▴ 90
1
vote
2
replies
2.7k
views
gene expression visualization: lineplot with ggplot2
ggplot2
lineplot
visualization
updated 9.0 years ago by
Jeremy Ng
▴ 180 • written 9.0 years ago by
alakatos
▴ 130
0
votes
2
replies
906
views
ANN: Bioconductor short course June 1-3 in Seattle
Preprocessing
Visualization
Cancer
Preprocessing
Visualization
Cancer
19.1 years ago
Seth Falcon
★ 7.4k
2
votes
2
replies
1.2k
views
Can't display protein domain data from UCSC table unipDomain using Gviz
Gviz
protein
visualization
UcscTrack
protein domains
updated 3.7 years ago by
James W. MacDonald
65k • written 3.7 years ago by
paul.jaschke
▴ 10
0
votes
2
replies
875
views
ggplot2 bar plot
R
Visualization
ggplot2
19 months ago
Jitendra
▴ 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 10.3 years ago by
Gordon Smyth
50k • written 10.3 years ago by
Heather Estrella
▴ 30
1
vote
2
replies
1.2k
views
Package for custom visualization of multiple sequence alignment
MSA
visualization
updated 5.6 years ago by
ulrich.bodenhofer
▴ 20 • written 5.6 years ago by
tim.ivanov.92
• 0
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 10.2 years ago by
Ming
▴ 380 • written 10.2 years ago by
Michael Love
42k
0
votes
2
replies
1.7k
views
Visualizing GOstats HyperGTest results
GO
Visualization
GOstats
GO
Visualization
GOstats
updated 16.3 years ago by
James W. MacDonald
65k • written 16.3 years ago by
Srinivas Iyyer
▴ 600
0
votes
2
replies
1.5k
views
FlowViz graphics problems
Microarray
Visualization
graph
flowCore
flowViz
Microarray
Visualization
graph
flowCore
updated 15.0 years ago by
Nishant Gopalakrishnan
▴ 340 • written 15.0 years ago by
Anja Schiel
▴ 20
0
votes
2
replies
1.4k
views
proposed: a bridge between R and Cytoscape
Visualization
Network
graph
Visualization
Network
graph
updated 13.9 years ago by
Steve Lianoglou
★ 13k • written 13.9 years ago by
Paul Shannon
★ 1.1k
0
votes
2
replies
2.6k
views
DESeq2 error
Visualization
Clustering
DESeq2
Visualization
Clustering
DESeq2
10.3 years ago
Michael Love
42k
0
votes
1
reply
1.3k
views
Survey on interactive visualization and Bioconductor
visualization
epivizr
7.9 years ago
Hector Corrada Bravo
▴ 60
2
votes
1
reply
3.5k
views
Heatmap function
Visualization
Visualization
updated 20.6 years ago by
Furge, Kyle
▴ 210 • written 20.6 years ago by
Marcus
▴ 150
0
votes
1
reply
1.5k
views
ChIPseeker gene body plot
chipseeker
visualization
updated 7.9 years ago by
Guangchuang Yu
★ 1.2k • written 7.9 years ago by
igor
▴ 40
0
votes
1
reply
1.0k
views
Several questions goCluster and GOstats...
Annotation
GO
Visualization
Yeast
goCluster
Annotation
GO
Visualization
Yeast
goCluster
updated 18.7 years ago by
Gunnar Wrobel
▴ 60 • written 18.7 years ago by
Lourdes Peña Castillo
▴ 140
0
votes
1
reply
724
views
comparative genomics
Visualization
Visualization
updated 18.9 years ago by
Sean Davis
21k • written 18.9 years ago by
Sorani, Marco
▴ 30
0
votes
1
reply
1.5k
views
Graphic representation of mroast results
mroast
visualization
8.9 years ago
Elena Serrano
▴ 30
0
votes
1
reply
1.4k
views
Talk & Poster - Final Call - qPCR 2009 Event
SNP
qPCR
Normalization
Visualization
Regression
Cancer
probe
PROcess
microRNA
SNP
qPCR
15.4 years ago
qPCR Platform - the reference in real-t…
▴ 170
0
votes
1
reply
1.0k
views
status of visnab
Visualization
ggbio
Gviz
Visualization
ggbio
Gviz
updated 11.0 years ago by
Tengfei Yin
▴ 420 • written 11.0 years ago by
Abhishek Pratap
▴ 410
50 results • Page
1 of 1
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Answer: Gene set enrichment analysis
by
Guido Hooiveld
★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
Comment: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
zzrammal
• 0
thank you for your response. The problem is resolved. When i did a fit for the linear model i put NULL for the design fit <- lmFit(count_…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ziliang
• 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont
by
Denis
• 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: minfi latest update for EPIC V2 chip
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
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