Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
visualization
•
reset
0
votes
0
replies
17k
views
1000 R tutorials/Links
Sequencing
Microarray
Genetics
Visualization
Network
Bayesian
Classification
Clustering
13.9 years ago
David Lyon
▴ 340
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
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
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
0
votes
1
reply
8.3k
views
Using DESeq normalized gene count to replace FPKM?
Visualization
DESeq
Visualization
DESeq
updated 10.8 years ago by
Simon Anders
★ 3.7k • written 10.8 years ago by
Jike Cui
▴ 10
11
votes
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
votes
0
replies
5.1k
views
Reading GFF files into R and GenomeGraphs
Coverage
Annotation
Visualization
convert
GLAD
GenomeGraphs
rtracklayer
IRanges
Coverage
14.8 years ago
Michael Dondrup
▴ 140
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
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
7
votes
0
replies
3.7k
views
Tutorial:
New edX "Data analysis for Life Sciences" module: High performance computing for reproducible genomics
annotation
genomicranges
visualization
docker
shiny
Tutorial
8.2 years ago
Vincent J. Carey, Jr.
6.7k
8
votes
0
replies
3.6k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
8.9 years ago
Martin Morgan
25k
2
votes
1
reply
3.5k
views
Heatmap function
Visualization
Visualization
updated 20.5 years ago by
Furge, Kyle
▴ 210 • written 20.5 years ago by
Marcus
▴ 150
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
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
0
votes
6
replies
3.3k
views
Fwd: WGCNA: labeledHeatmap and verboseScatterplot correlations and p-values are not the same
Visualization
Visualization
9.8 years ago
Peter Langfelder
★ 3.0k
0
votes
0
replies
3.2k
views
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
10.8 years ago
Luo Weijun
★ 1.6k
5
votes
11
replies
3.1k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
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
10.6 years ago
Luo Weijun
★ 1.6k
0
votes
6
replies
2.9k
views
Gviz::plotTracks for BiomartGeneRegionTrack() produces empty plots
gviz
visualization
9.3 years ago
Asta Laiho
▴ 120
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
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
0
replies
2.6k
views
Pathview with non-KEGG organisms?
Microbiome
Pathways
GO
Visualization
Organism
graph
gage
pathview
Microbiome
Pathways
GO
10.8 years ago
Luo Weijun
★ 1.6k
0
votes
2
replies
2.6k
views
DESeq2 error
Visualization
Clustering
DESeq2
Visualization
Clustering
DESeq2
10.3 years ago
Michael Love
42k
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
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
Marc Carlson
★ 7.2k • written 13.1 years ago by
Paolo Sonego
▴ 140
1
vote
1
reply
2.3k
views
Using DESeq2: experimental design and extracting results
Visualization
DESeq
DESeq2
Visualization
DESeq
DESeq2
updated 9.8 years ago by
Michael Love
42k • written 9.8 years ago by
bio2001
▴ 60
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
3
replies
2.3k
views
RNAseq read coverage plot: What tool?
rnaseq
visualization
plotcoveragehist
updated 7.0 years ago by
Ou, Jianhong
★ 1.3k • written 7.1 years ago by
alakatos
▴ 130
0
votes
7
replies
2.2k
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
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
votes
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
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
2
votes
1
reply
2.1k
views
ggbio: examples of overlaying multiple assay datasets
ggbio
visualization
ggbio
updated 9.6 years ago by
Panagiotis Moulos
▴ 30 • written 9.6 years ago by
Abhishek Pratap
▴ 190
0
votes
0
replies
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
2.0k
views
Entrez Gene ID to Probe Set Name
aCGH
Sequencing
miRNA
Microarray
Annotation
Normalization
GO
Preprocessing
Visualization
updated 15.6 years ago by
Marc Carlson
★ 7.2k • written 15.6 years ago by
McGee, Monnie
▴ 300
0
votes
0
replies
2.0k
views
Gviz: DataTrack heatmap
Visualization
Gviz
Visualization
Gviz
11.0 years ago
florian.hahne@novartis.com
★ 1.6k
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
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
0
votes
0
replies
1.9k
views
Gviz question
Visualization
rtracklayer
Gviz
Visualization
rtracklayer
Gviz
12.2 years ago
florian.hahne@novartis.com
★ 1.6k
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
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
0
replies
1.8k
views
qPCR Events and 30% Discount on qPCR workshops
miRNA
qPCR
Epigenetics
GO
Visualization
Network
probe
microRNA
miRNA
qPCR
Epigenetics
14.6 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 12.5 years ago by
Wolfgang Huber
★ 13k • written 12.5 years ago by
Guest User
★ 13k
0
votes
0
replies
1.8k
views
Job:
Post-Doctoral Research Fellow - Patient Genomics Data Visualization
visualization
genomics
personalized medicine
systemsbiology
js
Job
9.1 years ago
Hamid Bolouri
▴ 50
0
votes
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
10.6 years ago
Luo Weijun
★ 1.6k
3
votes
0
replies
1.7k
views
News:
BioCAsia, 8 Sept 2015, Tokyo
sequencing
transcription
epigenomics
visualization
infrastructure
News
8.9 years ago • updated 8.8 years ago
Matthew Ritchie
▴ 1000
0
votes
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
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
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
50 results • Page
1 of 1
Recent ...
Replies
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE
by
maria.soler
• 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Answer: Differential gene expression analysis results
by
ATpoint
★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Votes
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Awards
• All
Popular Question
to
maria.soler
• 0
Popular Question
to
Pietro
▴ 40
Popular Question
to
neilzhao
▴ 30
Popular Question
to
ATpoint
★ 4.1k
Teacher
to
Michael Love
42k
Locations
• All
United States,
just now
European Union,
6 minutes ago
France,
11 minutes ago
United States,
24 minutes ago
Egypt,
28 minutes ago
Traffic: 692 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6