Showing : Pathways • reset
2
votes
2
replies
144
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
6 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 ▴ 30
0
votes
0
replies
329
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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
421
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
706
views
Pathway Analysis using GAGE
gage RNASeq gageData Pathways
2.0 years ago OST • 0
1
vote
2
replies
801
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 ▴ 350 • written 3.1 years ago by ▴ 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 65k • written 3.4 years ago by • 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 ★ 3.2k • written 3.8 years ago by ▴ 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 25k • written 4.0 years ago by • 0
0
votes
4
replies
981
views
Fonction of genes/metabolites in a pathway?
gene metabolite functionnal annotation pathways
updated 4.1 years ago by ★ 3.9k • written 4.1 years ago by • 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
958
views
Help for Research Proposal
drug development pathways bioinformatics
updated 5.4 years ago by ★ 13k • written 5.4 years ago by • 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 • 0 • written 5.9 years ago by ▴ 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 ★ 1.2k • written 5.9 years ago by • 0
0
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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 • 0 • written 10.5 years ago by ★ 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 ★ 1.6k • written 7.0 years ago by • 0
0
votes
1
reply
2.0k
views
Pathview: visualization of data
pathways
updated 7.1 years ago by ★ 1.6k • written 7.1 years ago by • 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 ▴ 40 • written 7.6 years ago by • 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 • 0 • written 8.3 years ago by ▴ 20
2
votes
1
reply
1.1k
views
Problem with data not found using pathview package
pathways
updated 8.9 years ago by 65k • written 8.9 years ago by • 0
8
votes
14
replies
3.8k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 9.0 years ago by ▴ 150 • written 9.4 years ago by ★ 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 ▴ 150 • written 9.5 years ago by ★ 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 ★ 1.6k • written 9.1 years ago by ▴ 100
0
votes
13
replies
5.8k
views
gage pathways enrichment analysis
gage pathways kegg
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 100
0
votes
2
replies
4.4k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 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
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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 1 of 1
Recent ...
Replies
Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Votes
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
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