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Showing :
Pathways
•
reset
2
votes
2
replies
134
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
5 days ago
julia_mcdonough
• 0
0
votes
11
replies
2.0k
views
globaltest question
Pathways
probe
affy
Pathways
probe
affy
written 17.6 years ago by
mike Ad.
▴ 30
0
votes
0
replies
327
views
Job:
Postdoc for computational biology on cancer omics data analysis at Liang lab of Wistar Institute, Philadelphia, US
omics
cancerdata
Pathways
3 months ago
omicsresearch
• 0
0
votes
1
reply
477
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
11 months ago
Grace
• 0
0
votes
0
replies
420
views
Changing pathway names in pathway analysis
pathways
Pathways
14 months ago
Katharina
• 0
0
votes
0
replies
583
views
Job:
EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq
Transcriptomics
Pathways
Epigenetics
RNASeq
17 months ago
whduke
• 0
0
votes
0
replies
704
views
Pathway Analysis using GAGE
gage
RNASeq
gageData
Pathways
2.0 years ago
OST
• 0
1
vote
2
replies
800
views
Pathway analysis of RNAseq data using goseq package
Pathways
goseq
RNASeqData
2.1 years ago
m.glymenaki
• 0
0
votes
6
replies
3.6k
views
extracting the KEGG pathway for a set of genes
Pathways
KEGG
2.7 years ago
Bogdan
▴ 670
0
votes
4
replies
4.9k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R
Pathways
pheatmap
limma
updated 3.1 years ago by
SamGG
▴ 350 • written 3.1 years ago by
r.i.s.alnuwaysir
▴ 10
1
vote
1
reply
1.1k
views
News:
SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview
pathways
SBGNview.data
pathview
visualization
3.1 years ago
Luo Weijun
★ 1.6k
2
votes
0
replies
916
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq
GO
topGO
Pathways
3.2 years ago
Ben
▴ 50
2
votes
2
replies
1.1k
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
ojong
• 0
2
votes
1
reply
2.0k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 3.8 years ago by
Robert Castelo
★ 3.2k • written 3.8 years ago by
igor
▴ 40
0
votes
1
reply
1.7k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest
software error
pathways
modules
kegg
updated 4.0 years ago by
Martin Morgan
25k • written 4.0 years ago by
predeus
• 0
0
votes
4
replies
980
views
Fonction of genes/metabolites in a pathway?
gene
metabolite
functionnal annotation
pathways
updated 4.1 years ago by
Kevin Blighe
★ 3.9k • written 4.1 years ago by
emisecherre
• 0
0
votes
0
replies
763
views
plotting Signalling Pathways using SPIA
SPIA
functional-analysis
Pathways
KEGG
4.1 years ago
Assa Yeroslaviz
★ 1.5k
2
votes
2
replies
956
views
Help for Research Proposal
drug development
pathways
bioinformatics
updated 5.4 years ago by
Steve Lianoglou
★ 13k • written 5.4 years ago by
wajeehaejaz17
• 0
0
votes
0
replies
947
views
Pathview input error: non-numeric variable in data frame
pathview
kegg
pathways
package
5.5 years ago
anc.informatics
• 0
0
votes
0
replies
664
views
Interactive metabolic pathway
pathways
5.7 years ago
pritim2k6
• 0
0
votes
1
reply
977
views
Protein pathway analysis -- Classify, organize, and cluster a list of proteins / discovering relations between a set of proteins and linking them to …
protein
disease
pathway analysis
pathways
5.7 years ago
ረ
• 0
0
votes
0
replies
763
views
Could not find pathways in HSA gmt
pathways
gmt
5.9 years ago
flalix
• 0
0
votes
5
replies
5.7k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler
pathway analysis
pathways
updated 17 months ago by
yuhang
• 0 • written 5.9 years ago by
Mr.RB
▴ 20
2
votes
4
replies
2.1k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways
reactomepa
functional annotation
updated 5.9 years ago by
Guangchuang Yu
★ 1.2k • written 5.9 years ago by
martin.busch
• 0
0
votes
0
replies
1.0k
views
Pathview web - unable to map transcriptomic data
pathways
high-throughput transcriptomics
nonmodel species
6.0 years ago
monteiro
• 0
0
votes
0
replies
977
views
igraph PoTRA error
graph
pathways
igraph
6.1 years ago
genomic8328
▴ 10
2
votes
1
reply
1.9k
views
Pathview graph with multiple states/samples or time series
Pathways
graph
Pathways
graph
updated 6.2 years ago by
atanas.kamburov
• 0 • written 10.5 years ago by
Luo Weijun
★ 1.6k
0
votes
0
replies
1.2k
views
Two questions about pathifier package
pathways
statistics
microarray
6.3 years ago
arronar
• 0
1
vote
0
replies
1.4k
views
Job:
Bioinformatician/Computational Biologist - Dublin City, Ireland
bioinformatician job
computational biology
genomes
pathways
machine learning
Job
6.5 years ago
bulfin.triona
▴ 10
0
votes
1
reply
1.9k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R
GSEA
GAGE
pathways
updated 7.0 years ago by
Luo Weijun
★ 1.6k • written 7.0 years ago by
snishtala03
• 0
0
votes
1
reply
2.0k
views
Pathview: visualization of data
pathways
updated 7.1 years ago by
Luo Weijun
★ 1.6k • written 7.1 years ago by
svmichaela
• 0
0
votes
0
replies
1.2k
views
Pathway analysis for diffrential express gene
pathways
gage
annotation
gostats
7.1 years ago
avinash gupta
▴ 130
0
votes
0
replies
1.3k
views
Job:
PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job
phd
R
pathways
Job
7.3 years ago
Frank Kramer
▴ 60
0
votes
6
replies
1.5k
views
Is reactome.db still updated?
reactome.db
annotation
pathways
7.5 years ago
Guido Hooiveld
★ 3.9k
0
votes
4
replies
1.9k
views
EGSEA: how does the program generate the value for the up or down regulation of gene sets or pathways
pathways
gsea
egsea
gage
updated 7.6 years ago by
Monther Alhamdoosh
▴ 40 • written 7.6 years ago by
yingchen
• 0
2
votes
0
replies
1.4k
views
Job:
PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job
job
phd
R
pathways
Job
7.6 years ago
Frank Kramer
▴ 60
0
votes
2
replies
2.7k
views
WGCNA - Using real data for tutorial III
pathways
wgcna
network
rna-seq
8.3 years ago
hywel.williams
• 0
2
votes
3
replies
4.8k
views
Pathview None of the genes or compounds mapped to the pathway
pathview
pathways
KEGG
empty map
updated 2.7 years ago by
najib
• 0 • written 8.3 years ago by
Dani
▴ 20
2
votes
1
reply
1.1k
views
Problem with data not found using pathview package
pathways
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
nurhafizah.nazari
• 0
8
votes
14
replies
3.8k
views
reactome.db is not updated?
genesetenrichment
pathways
reactome.db
updated 9.0 years ago by
willem.ligtenberg
▴ 150 • written 9.4 years ago by
Guangchuang Yu
★ 1.2k
1
vote
15
replies
3.4k
views
reactome.db: reactome IDs not mapped to pathway names
annotation
pathways
updated 9.0 years ago by
willem.ligtenberg
▴ 150 • written 9.5 years ago by
Johannes Rainer
★ 2.0k
0
votes
2
replies
1.7k
views
retrieve kegg pathway abundances from gage analysis
gage
pathways
kegg
updated 9.1 years ago by
Luo Weijun
★ 1.6k • written 9.1 years ago by
francesca.defilippis
▴ 100
0
votes
13
replies
5.8k
views
gage pathways enrichment analysis
gage
pathways
kegg
updated 9.4 years ago by
Luo Weijun
★ 1.6k • written 9.4 years ago by
francesca.defilippis
▴ 100
0
votes
2
replies
4.4k
views
Pathway enrichment in bacteria metagenomes
pathways
metagenomics
updated 9.4 years ago by
Luo Weijun
★ 1.6k • written 9.4 years ago by
francesca.defilippis
▴ 100
0
votes
0
replies
2.3k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways
GO
Organism
GOstats
9.6 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.7k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways
GO
Organism
GOstats
9.6 years ago
Guest User
★ 13k
0
votes
0
replies
1.5k
views
Error in keggPathwayGraphs when updateCache = TRUE
Pathways
ROntoTools
Pathways
ROntoTools
9.7 years ago
Guest User
★ 13k
0
votes
0
replies
1.3k
views
ISMB talks: Pathview for pathway-based data integration and visualization
Pathways
Visualization
pathview
Pathways
Visualization
pathview
9.8 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.1k
views
ECCB 2014
Sequencing
Pathways
Sequencing
Pathways
9.9 years ago
Wolfgang Raffelsberger
▴ 60
0
votes
0
replies
1.4k
views
PostDoc opportunity
Pathways
Network
Pathways
Network
9.9 years ago
Guest User
★ 13k
50 results • Page
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Recent ...
Replies
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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