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Showing :
pathways
•
reset
1
vote
4
replies
301
views
pathview - multiple states
pathview
Pathways
KEGG
15 days ago • updated 14 days ago
Philippine
• 0
3
votes
1
reply
1.0k
views
Difference between enrichGO results and Enrichr website results
Pathways
GO.db
clusterProfiler
updated 5 months ago by
Guido Hooiveld
★ 4.1k • written 5 months ago by
adrip
▴ 10
1
vote
9
replies
1.5k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 6 months ago by
James W. MacDonald
67k • written 6 months ago by
adrip
▴ 10
2
votes
3
replies
894
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
updated 5 weeks ago by
josephasmith1310
• 0 • written 8 months ago by
julia_mcdonough
• 0
0
votes
11
replies
2.5k
views
globaltest question
Pathways
probe
affy
Pathways
probe
affy
written 18.3 years ago by
mike Ad.
▴ 30
0
votes
0
replies
607
views
Job:
Postdoc for computational biology on cancer omics data analysis at Liang lab of Wistar Institute, Philadelphia, US
omics
cancerdata
Pathways
11 months ago
omicsresearch
• 0
0
votes
1
reply
688
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation
missMethyl
Pathways
20 months ago
Grace
• 0
0
votes
0
replies
706
views
Changing pathway names in pathway analysis
pathways
Pathways
22 months ago
Katharina
• 0
0
votes
0
replies
835
views
Job:
EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq
Transcriptomics
Pathways
Epigenetics
RNASeq
2.1 years ago
whduke
• 0
0
votes
0
replies
980
views
Pathway Analysis using GAGE
gage
RNASeq
gageData
Pathways
2.7 years ago
OST
• 0
1
vote
2
replies
1.0k
views
Pathway analysis of RNAseq data using goseq package
Pathways
goseq
RNASeqData
2.8 years ago • updated 2.7 years ago
m.glymenaki
• 0
0
votes
6
replies
4.5k
views
extracting the KEGG pathway for a set of genes
Pathways
KEGG
3.4 years ago
Bogdan
▴ 670
0
votes
4
replies
6.0k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R
Pathways
pheatmap
limma
updated 3.7 years ago by
SamGG
▴ 360 • written 3.7 years ago by
r.i.s.alnuwaysir
▴ 10
1
vote
1
reply
1.3k
views
News:
SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview
pathways
SBGNview.data
pathview
visualization
3.8 years ago
Luo Weijun
★ 1.6k
2
votes
0
replies
1.2k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq
GO
topGO
Pathways
3.9 years ago
Ben
▴ 50
2
votes
2
replies
1.4k
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 4.0 years ago by
James W. MacDonald
67k • written 4.0 years ago by
ojong
• 0
2
votes
1
reply
2.6k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 4.4 years ago by
Robert Castelo
★ 3.4k • written 4.4 years ago by
igor
▴ 50
0
votes
1
reply
2.1k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest
software error
pathways
modules
kegg
updated 4.7 years ago by
Martin Morgan
25k • written 4.7 years ago by
predeus
• 0
0
votes
4
replies
1.2k
views
Fonction of genes/metabolites in a pathway?
gene
metabolite
functionnal annotation
pathways
updated 4.7 years ago by
Kevin Blighe
★ 4.0k • written 4.7 years ago by
emisecherre
• 0
0
votes
0
replies
973
views
plotting Signalling Pathways using SPIA
SPIA
functional-analysis
Pathways
KEGG
4.8 years ago
Assa Yeroslaviz
★ 1.5k
2
votes
2
replies
1.2k
views
Help for Research Proposal
drug development
pathways
bioinformatics
updated 6.0 years ago by
Steve Lianoglou
★ 13k • written 6.0 years ago by
wajeehaejaz17
• 0
0
votes
0
replies
1.1k
views
Pathview input error: non-numeric variable in data frame
pathview
kegg
pathways
package
6.2 years ago
anc.informatics
• 0
0
votes
0
replies
781
views
Interactive metabolic pathway
pathways
6.3 years ago
pritim2k6
• 0
0
votes
1
reply
1.2k
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
6.4 years ago
ረ
• 0
0
votes
0
replies
910
views
Could not find pathways in HSA gmt
pathways
gmt
6.5 years ago
flalix
• 0
0
votes
5
replies
6.6k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler
pathway analysis
pathways
updated 2.1 years ago by
yuhang
• 0 • written 6.6 years ago by
Mr.RB
▴ 20
2
votes
4
replies
2.6k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways
reactomepa
functional annotation
updated 6.6 years ago by
Guangchuang Yu
★ 1.2k • written 6.6 years ago by
martin.busch
• 0
0
votes
0
replies
1.3k
views
Pathview web - unable to map transcriptomic data
pathways
high-throughput transcriptomics
nonmodel species
6.7 years ago
monteiro
• 0
0
votes
0
replies
1.1k
views
igraph PoTRA error
graph
pathways
igraph
6.8 years ago
genomic8328
▴ 10
2
votes
1
reply
2.1k
views
Pathview graph with multiple states/samples or time series
Pathways
graph
Pathways
graph
updated 6.9 years ago by
atanas.kamburov
• 0 • written 11.2 years ago by
Luo Weijun
★ 1.6k
0
votes
0
replies
1.4k
views
Two questions about pathifier package
pathways
statistics
microarray
6.9 years ago
arronar
• 0
1
vote
0
replies
1.6k
views
Job:
Bioinformatician/Computational Biologist - Dublin City, Ireland
bioinformatician job
computational biology
genomes
pathways
machine learning
Job
7.2 years ago
bulfin.triona
▴ 10
0
votes
1
reply
2.1k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R
GSEA
GAGE
pathways
updated 7.6 years ago by
Luo Weijun
★ 1.6k • written 7.6 years ago by
snishtala03
• 0
0
votes
1
reply
2.3k
views
Pathview: visualization of data
pathways
updated 7.8 years ago by
Luo Weijun
★ 1.6k • written 7.8 years ago by
svmichaela
• 0
0
votes
0
replies
1.4k
views
Pathway analysis for diffrential express gene
pathways
gage
annotation
gostats
7.8 years ago
avinash gupta
▴ 130
0
votes
0
replies
1.5k
views
Job:
PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job
phd
R
pathways
Job
8.0 years ago
Frank Kramer
▴ 60
0
votes
6
replies
1.8k
views
Is reactome.db still updated?
reactome.db
annotation
pathways
8.2 years ago
Guido Hooiveld
★ 4.1k
0
votes
4
replies
2.2k
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 8.2 years ago by
Monther Alhamdoosh
▴ 40 • written 8.2 years ago by
yingchen
• 0
2
votes
0
replies
1.5k
views
Job:
PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job
job
phd
R
pathways
Job
8.2 years ago
Frank Kramer
▴ 60
0
votes
2
replies
3.0k
views
WGCNA - Using real data for tutorial III
pathways
wgcna
network
rna-seq
8.9 years ago
hywel.williams
• 0
2
votes
3
replies
5.4k
views
Pathview None of the genes or compounds mapped to the pathway
pathview
pathways
KEGG
empty map
updated 3.4 years ago by
najib
• 0 • written 9.0 years ago by
Dani
▴ 20
2
votes
1
reply
1.3k
views
Problem with data not found using pathview package
pathways
updated 9.6 years ago by
James W. MacDonald
67k • written 9.6 years ago by
nurhafizah.nazari
• 0
8
votes
14
replies
4.3k
views
reactome.db is not updated?
genesetenrichment
pathways
reactome.db
updated 9.7 years ago by
willem.ligtenberg
▴ 150 • written 10.1 years ago by
Guangchuang Yu
★ 1.2k
1
vote
15
replies
4.0k
views
reactome.db: reactome IDs not mapped to pathway names
annotation
pathways
updated 9.7 years ago by
willem.ligtenberg
▴ 150 • written 10.1 years ago by
Johannes Rainer
★ 2.1k
0
votes
2
replies
2.0k
views
retrieve kegg pathway abundances from gage analysis
gage
pathways
kegg
updated 9.8 years ago by
Luo Weijun
★ 1.6k • written 9.8 years ago by
francesca.defilippis
▴ 100
0
votes
13
replies
6.4k
views
gage pathways enrichment analysis
gage
pathways
kegg
updated 10.0 years ago by
Luo Weijun
★ 1.6k • written 10.1 years ago by
francesca.defilippis
▴ 100
0
votes
2
replies
4.9k
views
Pathway enrichment in bacteria metagenomes
pathways
metagenomics
updated 10.1 years ago by
Luo Weijun
★ 1.6k • written 10.1 years ago by
francesca.defilippis
▴ 100
0
votes
0
replies
2.5k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways
GO
Organism
GOstats
10.3 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.9k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways
GO
Organism
GOstats
10.3 years ago
Guest User
★ 13k
0
votes
0
replies
1.7k
views
Error in keggPathwayGraphs when updateCache = TRUE
Pathways
ROntoTools
Pathways
ROntoTools
10.4 years ago
Guest User
★ 13k
50 results • Page
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Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
James W. MacDonald
67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
anna.cot.anna.cot
▴ 30
Thank you James, that really helped! I tried CODE `enter code here` but I must have dome it incorrectly, as it showed all in red.
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
James W. MacDonald
67k
Please come back to the support site and view your post - I've fixed it for you. If you want to show people your targets file, just paste t…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
anna.cot.anna.cot
▴ 30
Thank you Gordon! Apologies if this is a too basic question-I'm a biologist and want to ensure I understand correctly. Here is my metadata …
Comment: nightmare to make custom txdb for genomes from ToxoDB
by
rohitsatyam102
▴ 20
I offer my apologies if the title was misleading. I will change it at once. I wrote txdb because the error emnated from `seqlevelsStyle(txd…
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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