Showing : Pathways • reset
1
vote
4
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880
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pathview - multiple states
pathview Pathways KEGG
11 months ago Philippine • 0
3
votes
1
reply
2.0k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 16 months ago by ★ 4.1k • written 16 months ago by ▴ 10
1
vote
9
replies
3.2k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 17 months ago by 68k • written 17 months ago by ▴ 10
2
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4
replies
2.3k
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 19 months ago by • 0
0
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11
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3.0k
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globaltest question
Pathways probe affy Pathways probe affy
written 19.2 years ago by ▴ 30
0
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0
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982
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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
22 months ago omicsresearch • 0
0
votes
1
reply
953
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation missMethyl Pathways
2.5 years ago Grace • 0
0
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0
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946
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Changing pathway names in pathway analysis
pathways Pathways
2.8 years ago Katharina • 0
0
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0
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1.1k
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Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
3.0 years ago whduke • 0
0
votes
0
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1.2k
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
3.6 years ago OST • 0
1
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2
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1.4k
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
3.7 years ago • updated 3.6 years ago m.glymenaki • 0
0
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6
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6.7k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
4.3 years ago Bogdan ▴ 670
0
votes
5
replies
7.4k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
written 4.6 years ago by ▴ 10
1
vote
1
reply
1.7k
views
News: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview pathways SBGNview.data pathview visualization
4.7 years ago Luo Weijun ★ 1.6k
2
votes
0
replies
1.5k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.8 years ago Ben ▴ 50
2
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2
replies
1.7k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
2
votes
1
reply
3.4k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 5.3 years ago by ★ 3.4k • written 5.3 years ago by ▴ 50
0
votes
1
reply
2.7k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
0
votes
4
replies
1.6k
views
Fonction of genes/metabolites in a pathway?
gene metabolite functionnal annotation pathways
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by • 0
0
votes
0
replies
1.2k
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
5.7 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
1.4k
views
Help for Research Proposal
drug development pathways bioinformatics
updated 6.9 years ago by ★ 13k • written 6.9 years ago by • 0
0
votes
0
replies
1.3k
views
Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
7.1 years ago anc.informatics • 0
0
votes
0
replies
904
views
Interactive metabolic pathway
pathways
7.2 years ago pritim2k6 • 0
0
votes
1
reply
1.5k
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
7.3 years ago ረ • 0
0
votes
0
replies
1.1k
views
Could not find pathways in HSA gmt
pathways gmt
7.4 years ago flalix • 0
0
votes
5
replies
7.5k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 3.0 years ago by • 0 • written 7.5 years ago by ▴ 20
2
votes
4
replies
3.1k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 7.5 years ago by ★ 1.2k • written 7.5 years ago by • 0
0
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0
replies
1.5k
views
Pathview web - unable to map transcriptomic data
pathways high-throughput transcriptomics nonmodel species
7.6 years ago monteiro • 0
0
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0
replies
1.4k
views
igraph PoTRA error
graph pathways igraph
7.7 years ago genomic8328 ▴ 10
2
votes
1
reply
2.4k
views
Pathview graph with multiple states/samples or time series
Pathways graph Pathways graph
updated 7.8 years ago by • 0 • written 12.1 years ago by ★ 1.6k
0
votes
0
replies
1.6k
views
Two questions about pathifier package
pathways statistics microarray
7.8 years ago arronar • 0
1
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0
replies
1.9k
views
Job: Bioinformatician/Computational Biologist - Dublin City, Ireland
bioinformatician job computational biology genomes pathways machine learning Job
8.1 years ago bulfin.triona ▴ 10
0
votes
1
reply
2.4k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 8.5 years ago by ★ 1.6k • written 8.5 years ago by • 0
0
votes
1
reply
2.7k
views
Pathview: visualization of data
pathways
updated 8.7 years ago by ★ 1.6k • written 8.7 years ago by • 0
0
votes
0
replies
1.6k
views
Pathway analysis for diffrential express gene
pathways gage annotation gostats
8.7 years ago avinash gupta ▴ 130
0
votes
0
replies
1.7k
views
Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job phd R pathways Job
8.9 years ago Frank Kramer ▴ 60
0
votes
6
replies
2.1k
views
Is reactome.db still updated?
reactome.db annotation pathways
9.1 years ago Guido Hooiveld ★ 4.1k
0
votes
4
replies
2.6k
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 9.1 years ago by ▴ 40 • written 9.1 years ago by • 0
2
votes
0
replies
1.7k
views
Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job job phd R pathways Job
9.2 years ago Frank Kramer ▴ 60
0
votes
2
replies
3.3k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
9.8 years ago hywel.williams • 0
2
votes
3
replies
5.9k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 4.3 years ago by • 0 • written 9.9 years ago by ▴ 20
2
votes
1
reply
1.4k
views
Problem with data not found using pathview package
pathways
updated 10.5 years ago by 68k • written 10.5 years ago by • 0
8
votes
14
replies
5.1k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 10.6 years ago by ▴ 150 • written 11.0 years ago by ★ 1.2k
1
vote
15
replies
4.7k
views
reactome.db: reactome IDs not mapped to pathway names
annotation pathways
updated 10.6 years ago by ▴ 150 • written 11.0 years ago by ★ 2.1k
0
votes
2
replies
2.2k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 10.7 years ago by ★ 1.6k • written 10.7 years ago by ▴ 100
0
votes
13
replies
7.1k
views
gage pathways enrichment analysis
gage pathways kegg
updated 11.0 years ago by ★ 1.6k • written 11.0 years ago by ▴ 100
0
votes
2
replies
5.3k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 11.0 years ago by ★ 1.6k • written 11.0 years ago by ▴ 100
0
votes
0
replies
2.6k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
11.2 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
2.1k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
11.2 years ago Guest User ★ 13k
0
votes
0
replies
1.9k
views
Error in keggPathwayGraphs when updateCache = TRUE
Pathways ROntoTools Pathways ROntoTools
11.3 years ago Guest User ★ 13k
246 results • Page 1 of 5
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Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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