Showing : Pathways • reset
1
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4
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pathview - multiple states
pathview Pathways KEGG
4 months ago Philippine • 0
3
votes
1
reply
1.6k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
1
vote
9
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2.5k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 10 months ago by 68k • written 10 months ago by ▴ 10
2
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4
replies
1.7k
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 12 months ago by • 0
0
votes
11
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2.7k
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globaltest question
Pathways probe affy Pathways probe affy
written 18.6 years ago by ▴ 30
0
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0
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715
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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
15 months ago omicsresearch • 0
0
votes
1
reply
800
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topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation missMethyl Pathways
24 months ago Grace • 0
0
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0
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815
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Changing pathway names in pathway analysis
pathways Pathways
2.2 years ago Katharina • 0
0
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0
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907
views
Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
2.4 years ago whduke • 0
0
votes
0
replies
1.1k
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
3.0 years ago OST • 0
1
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2
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1.2k
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
3.1 years ago m.glymenaki • 0
0
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6
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5.7k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
3.7 years ago Bogdan ▴ 670
0
votes
4
replies
6.7k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
updated 4.1 years ago by ▴ 360 • written 4.1 years ago by ▴ 10
1
vote
1
reply
1.4k
views
News: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview pathways SBGNview.data pathview visualization
4.1 years ago Luo Weijun ★ 1.6k
2
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0
replies
1.3k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.2 years ago Ben ▴ 50
2
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2
replies
1.5k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
2
votes
1
reply
3.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.8 years ago by ★ 3.4k • written 4.8 years ago by ▴ 50
0
votes
1
reply
2.4k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 5.0 years ago by 25k • written 5.0 years ago by • 0
0
votes
4
replies
1.4k
views
Fonction of genes/metabolites in a pathway?
gene metabolite functionnal annotation pathways
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
0
votes
0
replies
1.0k
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
5.1 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
1.3k
views
Help for Research Proposal
drug development pathways bioinformatics
updated 6.4 years ago by ★ 13k • written 6.4 years ago by • 0
0
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0
replies
1.2k
views
Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
6.6 years ago anc.informatics • 0
0
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0
replies
830
views
Interactive metabolic pathway
pathways
6.7 years ago pritim2k6 • 0
0
votes
1
reply
1.3k
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
6.8 years ago ረ • 0
0
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0
replies
978
views
Could not find pathways in HSA gmt
pathways gmt
6.9 years ago flalix • 0
0
votes
5
replies
7.0k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 2.5 years ago by • 0 • written 6.9 years ago by ▴ 20
2
votes
4
replies
2.9k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by • 0
0
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0
replies
1.4k
views
Pathview web - unable to map transcriptomic data
pathways high-throughput transcriptomics nonmodel species
7.0 years ago monteiro • 0
0
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0
replies
1.2k
views
igraph PoTRA error
graph pathways igraph
7.1 years ago genomic8328 ▴ 10
2
votes
1
reply
2.2k
views
Pathview graph with multiple states/samples or time series
Pathways graph Pathways graph
updated 7.2 years ago by • 0 • written 11.5 years ago by ★ 1.6k
0
votes
0
replies
1.5k
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Two questions about pathifier package
pathways statistics microarray
7.3 years ago arronar • 0
1
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0
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1.7k
views
Job: Bioinformatician/Computational Biologist - Dublin City, Ireland
bioinformatician job computational biology genomes pathways machine learning Job
7.5 years ago bulfin.triona ▴ 10
0
votes
1
reply
2.3k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 8.0 years ago by ★ 1.6k • written 8.0 years ago by • 0
0
votes
1
reply
2.5k
views
Pathview: visualization of data
pathways
updated 8.1 years ago by ★ 1.6k • written 8.1 years ago by • 0
0
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0
replies
1.5k
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Pathway analysis for diffrential express gene
pathways gage annotation gostats
8.2 years ago avinash gupta ▴ 130
0
votes
0
replies
1.6k
views
Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job phd R pathways Job
8.4 years ago Frank Kramer ▴ 60
0
votes
6
replies
1.9k
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Is reactome.db still updated?
reactome.db annotation pathways
8.5 years ago Guido Hooiveld ★ 4.1k
0
votes
4
replies
2.4k
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 8.6 years ago by ▴ 40 • written 8.6 years ago by • 0
2
votes
0
replies
1.6k
views
Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job job phd R pathways Job
8.6 years ago Frank Kramer ▴ 60
0
votes
2
replies
3.1k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
9.3 years ago hywel.williams • 0
2
votes
3
replies
5.6k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 3.8 years ago by • 0 • written 9.3 years ago by ▴ 20
2
votes
1
reply
1.3k
views
Problem with data not found using pathview package
pathways
updated 9.9 years ago by 68k • written 9.9 years ago by • 0
8
votes
14
replies
4.7k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 10.1 years ago by ▴ 150 • written 10.4 years ago by ★ 1.2k
1
vote
15
replies
4.3k
views
reactome.db: reactome IDs not mapped to pathway names
annotation pathways
updated 10.1 years ago by ▴ 150 • written 10.5 years ago by ★ 2.1k
0
votes
2
replies
2.1k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 10.1 years ago by ★ 1.6k • written 10.2 years ago by ▴ 100
0
votes
13
replies
6.7k
views
gage pathways enrichment analysis
gage pathways kegg
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by ▴ 100
0
votes
2
replies
5.1k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by ▴ 100
0
votes
0
replies
2.5k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
10.6 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
2.0k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
10.6 years ago Guest User ★ 13k
0
votes
0
replies
1.8k
views
Error in keggPathwayGraphs when updateCache = TRUE
Pathways ROntoTools Pathways ROntoTools
10.7 years ago Guest User ★ 13k
50 results • Page 1 of 1
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Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Votes
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
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