Showing : pathways • reset
2
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2
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168
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
13 days ago julia_mcdonough • 0
0
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11
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2.0k
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globaltest question
Pathways probe affy Pathways probe affy
written 17.6 years ago by ▴ 30
0
votes
0
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343
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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
486
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topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation missMethyl Pathways
12 months ago Grace • 0
0
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0
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434
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Changing pathway names in pathway analysis
pathways Pathways
15 months ago Katharina • 0
0
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0
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592
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Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
17 months ago whduke • 0
0
votes
5
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5.7k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 18 months ago by • 0 • written 5.9 years ago by ▴ 20
0
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3
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4.8k
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how to get gene list for given GO terms?
Pathways GO Cancer PROcess goTools genomes Pathways GO Cancer PROcess goTools genomes
updated 22 months ago by • 0 • written 12.2 years ago by ★ 7.2k
0
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0
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717
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
2.0 years ago OST • 0
1
vote
2
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812
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
2.1 years ago m.glymenaki • 0
0
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6
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3.7k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
2.7 years ago Bogdan ▴ 670
2
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3
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4.8k
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Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 2.8 years ago by • 0 • written 8.3 years ago by ▴ 20
0
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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
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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
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0
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926
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
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2
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1.1k
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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
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 3.8 years ago by ★ 3.3k • written 3.8 years ago by ▴ 40
0
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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
992
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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
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0
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772
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.1 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
964
views
Help for Research Proposal
drug development pathways bioinformatics
updated 5.4 years ago by ★ 13k • written 5.4 years ago by • 0
0
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0
replies
957
views
Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
5.6 years ago anc.informatics • 0
0
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0
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671
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Interactive metabolic pathway
pathways
5.7 years ago pritim2k6 • 0
0
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1
reply
983
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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
5.8 years ago ረ • 0
0
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0
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767
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Could not find pathways in HSA gmt
pathways gmt
5.9 years ago flalix • 0
2
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4
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2.2k
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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
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0
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983
views
igraph PoTRA error
graph pathways igraph
6.1 years ago genomic8328 ▴ 10
2
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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
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0
replies
1.2k
views
Two questions about pathifier package
pathways statistics microarray
6.3 years ago arronar • 0
1
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0
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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
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1
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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
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1
reply
2.0k
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Pathview: visualization of data
pathways
updated 7.1 years ago by ★ 1.6k • written 7.1 years ago by • 0
0
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0
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1.2k
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Pathway analysis for diffrential express gene
pathways gage annotation gostats
7.2 years ago avinash gupta ▴ 130
0
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0
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1.3k
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Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job phd R pathways Job
7.4 years ago Frank Kramer ▴ 60
0
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6
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1.5k
views
Is reactome.db still updated?
reactome.db annotation pathways
7.5 years ago Guido Hooiveld ★ 3.9k
0
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4
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1.9k
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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
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0
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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
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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
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14
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3.8k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 9.1 years ago by ▴ 150 • written 9.4 years ago by ★ 1.2k
1
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15
replies
3.4k
views
reactome.db: reactome IDs not mapped to pathway names
annotation pathways
updated 9.1 years ago by ▴ 150 • written 9.5 years ago by ★ 2.0k
0
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2
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1.7k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 9.2 years ago by ★ 1.6k • written 9.2 years ago by ▴ 100
0
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13
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5.8k
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gage pathways enrichment analysis
gage pathways kegg
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 100
0
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2
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4.4k
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Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 100
0
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0
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2.3k
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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
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1.7k
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Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
9.6 years ago Guest User ★ 13k
0
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0
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1.5k
views
Error in keggPathwayGraphs when updateCache = TRUE
Pathways ROntoTools Pathways ROntoTools
9.7 years ago Guest User ★ 13k
0
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0
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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
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0
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1.1k
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ECCB 2014
Sequencing Pathways Sequencing Pathways
9.9 years ago Wolfgang Raffelsberger ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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