Showing : Pathways • reset
0
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6
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468
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extracting the KEGG pathway for a set of genes
Pathways KEGG
5 months ago Bogdan ▴ 620
0
votes
4
replies
1.3k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
updated 10 months ago by ▴ 270 • written 10 months ago by ▴ 10
1
vote
1
reply
365
views
News: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview pathways SBGNview.data pathview visualization
11 months ago • updated 10 months ago Luo Weijun ★ 1.5k
2
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0
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212
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Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
12 months ago Ben ▴ 30
2
votes
2
replies
354
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 13 months ago by 58k • written 13 months ago by • 0
2
votes
1
reply
489
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 18 months ago by ★ 2.8k • written 18 months ago by ▴ 40
0
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1
reply
248
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 21 months ago by 25k • written 21 months ago by • 0
0
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4
replies
280
views
Fonction of genes/metabolites in a pathway?
gene metabolite functionnal annotation pathways
updated 22 months ago by 3.4k • written 22 months ago by • 0
0
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0
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205
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
22 months ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
414
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Help for Research Proposal
drug development pathways bioinformatics
updated 3.2 years ago by 13k • written 3.2 years ago by • 0
0
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0
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469
views
Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
3.3 years ago anc.informatics • 0
0
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0
replies
319
views
Interactive metabolic pathway
pathways
3.4 years ago pritim2k6 • 0
0
votes
1
reply
478
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
3.5 years ago ረ • 0
0
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0
replies
383
views
Could not find pathways in HSA gmt
pathways gmt
3.6 years ago flalix • 0
0
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4
replies
2.6k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 3.7 years ago by ★ 1.2k • written 3.7 years ago by ▴ 20
2
votes
4
replies
944
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 3.7 years ago by ★ 1.2k • written 3.7 years ago by • 0
0
votes
0
replies
505
views
Pathview web - unable to map transcriptomic data
pathways high-throughput transcriptomics nonmodel species
3.8 years ago monteiro • 0
0
votes
0
replies
492
views
igraph PoTRA error
graph pathways igraph
3.9 years ago genomic8328 ▴ 10
2
votes
1
reply
1.1k
views
Pathview graph with multiple states/samples or time series
Pathways graph Pathways graph
updated 4.0 years ago by • 0 • written 8.3 years ago by ★ 1.5k
0
votes
0
replies
539
views
Two questions about pathifier package
pathways statistics microarray
4.0 years ago arronar • 0
1
vote
0
replies
741
views
Job: Bioinformatician/Computational Biologist - Dublin City, Ireland
bioinformatician job computational biology genomes pathways machine learning Job
4.3 years ago bulfin.triona ▴ 10
0
votes
1
reply
1.2k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 4.7 years ago by ★ 1.5k • written 4.7 years ago by • 0
0
votes
1
reply
1.2k
views
Pathview: visualization of data
pathways
updated 4.9 years ago by ★ 1.5k • written 4.9 years ago by • 0
0
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0
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702
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Pathway analysis for diffrential express gene
pathways gage annotation gostats
4.9 years ago avinash gupta ▴ 130
0
votes
0
replies
788
views
Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job phd R pathways Job
5.1 years ago Frank Kramer ▴ 60
0
votes
6
replies
815
views
Is reactome.db still updated?
reactome.db annotation pathways
5.3 years ago Guido Hooiveld ★ 3.2k
0
votes
4
replies
1.1k
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 5.3 years ago by ▴ 40 • written 5.3 years ago by • 0
2
votes
0
replies
918
views
Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job job phd R pathways Job
5.4 years ago Frank Kramer ▴ 60
0
votes
2
replies
1.8k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
6.0 years ago hywel.williams • 0
1
vote
3
replies
2.9k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 6 months ago by • 0 • written 6.1 years ago by ▴ 10
2
votes
1
reply
752
views
Problem with data not found using pathview package
pathways
updated 6.7 years ago by 58k • written 6.7 years ago by • 0
8
votes
14
replies
2.5k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 6.8 years ago by ▴ 150 • written 7.2 years ago by ★ 1.2k
1
vote
15
replies
2.1k
views
reactome.db: reactome IDs not mapped to pathway names
annotation pathways
updated 6.8 years ago by ▴ 150 • written 7.2 years ago by ★ 1.9k
0
votes
2
replies
1.2k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 6.9 years ago by ★ 1.5k • written 6.9 years ago by ▴ 70
0
votes
13
replies
4.5k
views
gage pathways enrichment analysis
gage pathways kegg
updated 7.2 years ago by ★ 1.5k • written 7.2 years ago by ▴ 70
0
votes
2
replies
3.5k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 7.2 years ago by ★ 1.5k • written 7.2 years ago by ▴ 70
0
votes
0
replies
1.7k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
7.4 years ago Luo Weijun ★ 1.5k
0
votes
0
replies
1.1k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
7.4 years ago Guest User ★ 12k
0
votes
0
replies
1.0k
views
Error in keggPathwayGraphs when updateCache = TRUE
Pathways ROntoTools Pathways ROntoTools
7.5 years ago Guest User ★ 12k
0
votes
0
replies
865
views
ISMB talks: Pathview for pathway-based data integration and visualization
Pathways Visualization pathview Pathways Visualization pathview
7.6 years ago Luo Weijun ★ 1.5k
0
votes
0
replies
675
views
ECCB 2014
Sequencing Pathways Sequencing Pathways
7.7 years ago Wolfgang Raffelsberger ▴ 60
0
votes
0
replies
929
views
PostDoc opportunity
Pathways Network Pathways Network
7.7 years ago Guest User ★ 12k
0
votes
0
replies
629
views
Thalassiosira pseudonana
Annotation Pathways GO Annotation Pathways GO
7.7 years ago nooshin ▴ 300
0
votes
0
replies
708
views
graphite biopax conversion code?
Pathways graphite Pathways graphite
7.7 years ago Ryan C. Thompson 7.7k
0
votes
1
reply
959
views
Can GAGE be used for transcript set pathway analysis
Pathways gage Pathways gage
updated 7.7 years ago by ★ 1.5k • written 7.7 years ago by ▴ 100
0
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5
replies
2.2k
views
use of voom function with attract package
Pathways GO attract Pathways GO attract
updated 7.8 years ago by 44k • written 7.8 years ago by ★ 12k
0
votes
0
replies
867
views
KEGG pathway analysis with ReportingTools
Pathways GO ReportingTools Pathways GO ReportingTools
7.8 years ago Mayte Suarez-Farinas ▴ 510
0
votes
0
replies
1.1k
views
[phenoTest package]: gsea.kegg error with absVals parameter
Pathways GO hgu133a hgu95av2 phenoTest Pathways GO hgu133a hgu95av2 phenoTest
7.8 years ago Kostas Kerkentzes ▴ 10
0
votes
0
replies
1.1k
views
pathview with tomato and minor species
Pathways pathview Pathways pathview
7.9 years ago Luo Weijun ★ 1.5k
0
votes
0
replies
1.6k
views
GAGE/Pathview RNA-Seq Workflows: reference genome issue
Pathways pathview Pathways pathview
7.9 years ago Luo Weijun ★ 1.5k
50 results • Page 1 of 1
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Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Matthew • 0
Thanks for the suggestion, I'll give that a try! Based on the PCA, all three factors do tend to influence the results, so I'll try the colu…
Comment: fgsea not downloading due to new r version. Is there a way around this? by amir.khan • 0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Michael Love 35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
Answer: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
Comment: Unable to install Rhtslib in R-4.1.1 by cf2209 • 0
Thank you for your input I appreciate it. I will revise and make changes to this post as you suggested. Unfortunately I am not able to do t…
Votes
Answer: fgsea not downloading due to new r version. Is there a way around this?
Comment: Unable to install Rhtslib in R-4.1.1
Answer: fgsea not downloading due to new r version. Is there a way around this?
Answer: Swish with more than two conditions. Add support for contrasts?
Answer: ERROR: unable to find an inherited method for function ‘dispersions<-’ for signa
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