Showing : pathways • reset
3
votes
1
reply
840
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 4 months ago by ★ 4.1k • written 4 months ago by ▴ 10
1
vote
9
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1.3k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 5 months ago by 67k • written 5 months ago by ▴ 10
2
votes
3
replies
769
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
updated 5 days ago by • 0 • written 7 months ago by • 0
0
votes
11
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2.4k
views
globaltest question
Pathways probe affy Pathways probe affy
written 18.2 years ago by ▴ 30
0
votes
0
replies
585
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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
10 months ago omicsresearch • 0
0
votes
1
reply
667
views
topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation missMethyl Pathways
18 months ago Grace • 0
0
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0
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680
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Changing pathway names in pathway analysis
pathways Pathways
21 months ago Katharina • 0
0
votes
0
replies
820
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Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
2.0 years ago whduke • 0
0
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0
replies
952
views
Pathway Analysis using GAGE
gage RNASeq gageData Pathways
2.6 years ago OST • 0
1
vote
2
replies
1.0k
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
2.7 years ago • updated 2.6 years ago m.glymenaki • 0
0
votes
6
replies
4.3k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
3.3 years ago Bogdan ▴ 670
0
votes
4
replies
5.8k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
updated 3.6 years ago by ▴ 350 • written 3.6 years ago by ▴ 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
3.7 years ago Luo Weijun ★ 1.6k
2
votes
0
replies
1.1k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
3.8 years ago Ben ▴ 50
2
votes
2
replies
1.3k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.9 years ago by 67k • written 4.0 years ago by • 0
2
votes
1
reply
2.6k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.3 years ago by ★ 3.4k • written 4.3 years ago by ▴ 50
0
votes
1
reply
2.1k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.6 years ago by 25k • written 4.6 years ago by • 0
0
votes
4
replies
1.2k
views
Fonction of genes/metabolites in a pathway?
gene metabolite functionnal annotation pathways
updated 4.6 years ago by ★ 4.0k • written 4.7 years ago by • 0
0
votes
0
replies
958
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.7 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
1.1k
views
Help for Research Proposal
drug development pathways bioinformatics
updated 6.0 years ago by ★ 13k • written 6.0 years ago by • 0
0
votes
0
replies
1.1k
views
Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
6.1 years ago anc.informatics • 0
0
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0
replies
770
views
Interactive metabolic pathway
pathways
6.2 years ago pritim2k6 • 0
0
votes
1
reply
1.1k
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
6.3 years ago ረ • 0
0
votes
0
replies
899
views
Could not find pathways in HSA gmt
pathways gmt
6.4 years ago flalix • 0
0
votes
5
replies
6.5k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 2.1 years ago by • 0 • written 6.5 years ago by ▴ 20
2
votes
4
replies
2.5k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by • 0
0
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0
replies
1.2k
views
Pathview web - unable to map transcriptomic data
pathways high-throughput transcriptomics nonmodel species
6.6 years ago monteiro • 0
0
votes
0
replies
1.1k
views
igraph PoTRA error
graph pathways igraph
6.7 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 6.8 years ago by • 0 • written 11.1 years ago by ★ 1.6k
0
votes
0
replies
1.3k
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
7.1 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 7.5 years ago by ★ 1.6k • written 7.5 years ago by • 0
0
votes
1
reply
2.3k
views
Pathview: visualization of data
pathways
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by • 0
0
votes
0
replies
1.4k
views
Pathway analysis for diffrential express gene
pathways gage annotation gostats
7.7 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
7.9 years ago Frank Kramer ▴ 60
0
votes
6
replies
1.7k
views
Is reactome.db still updated?
reactome.db annotation pathways
8.1 years ago Guido Hooiveld ★ 4.1k
0
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4
replies
2.1k
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 8.1 years ago by ▴ 40 • written 8.1 years ago by • 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
2.9k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
8.8 years ago hywel.williams • 0
2
votes
3
replies
5.3k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 3.3 years ago by • 0 • written 8.9 years ago by ▴ 20
2
votes
1
reply
1.3k
views
Problem with data not found using pathview package
pathways
updated 9.5 years ago by 67k • written 9.5 years ago by • 0
8
votes
14
replies
4.2k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 9.6 years ago by ▴ 150 • written 10.0 years ago by ★ 1.2k
1
vote
15
replies
3.9k
views
reactome.db: reactome IDs not mapped to pathway names
annotation pathways
updated 9.6 years ago by ▴ 150 • written 10.0 years ago by ★ 2.1k
0
votes
2
replies
1.9k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 9.7 years ago by ★ 1.6k • written 9.7 years ago by ▴ 100
0
votes
13
replies
6.3k
views
gage pathways enrichment analysis
gage pathways kegg
updated 10.0 years ago by ★ 1.6k • written 10.0 years ago by ▴ 100
0
votes
2
replies
4.8k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 10.0 years ago by ★ 1.6k • written 10.0 years ago by ▴ 100
0
votes
0
replies
2.4k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
10.2 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.8k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
10.2 years ago Guest User ★ 13k
0
votes
0
replies
1.7k
views
Error in keggPathwayGraphs when updateCache = TRUE
Pathways ROntoTools Pathways ROntoTools
10.3 years ago Guest User ★ 13k
0
votes
0
replies
1.4k
views
ISMB talks: Pathview for pathway-based data integration and visualization
Pathways Visualization pathview Pathways Visualization pathview
10.4 years ago Luo Weijun ★ 1.6k
50 results • Page 1 of 1
Recent ...
Replies
Comment: [How to construct a model.matrix ] by kyj2226 • 0
Thanks to you, I learn a lot. Many thanks, Yujin.
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
thank you for your advice, I posted separate post.
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by Robert Castelo ★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Answer: DESeq2 rerun returns different results by ATpoint ★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Votes
Answer: [How to construct a model.matrix ]
C: DESeq2 baseMean values for each sample
C: DESeq2 baseMean values for each sample
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta
A: Some questions for remove batch effect by using mnnCorrect
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