Showing : pathways • reset
1
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4
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433
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pathview - multiple states
pathview Pathways KEGG
8 weeks ago Philippine • 0
3
votes
1
reply
1.2k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 7 months ago by ★ 4.1k • written 7 months ago by ▴ 10
1
vote
9
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1.8k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 7 months ago by 67k • written 7 months ago by ▴ 10
2
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3
replies
1.1k
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
updated 11 weeks ago by • 0 • written 9 months ago by • 0
0
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11
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2.5k
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globaltest question
Pathways probe affy Pathways probe affy
written 18.4 years ago by ▴ 30
0
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0
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646
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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
13 months ago omicsresearch • 0
0
votes
1
reply
729
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topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation missMethyl Pathways
21 months ago Grace • 0
0
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0
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739
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Changing pathway names in pathway analysis
pathways Pathways
2.0 years ago Katharina • 0
0
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0
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873
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Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
2.2 years ago whduke • 0
0
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0
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1.0k
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
2.8 years ago OST • 0
1
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2
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1.1k
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
2.9 years ago m.glymenaki • 0
0
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6
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4.8k
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extracting the KEGG pathway for a set of genes
Pathways KEGG
3.5 years ago Bogdan ▴ 670
0
votes
4
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6.1k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
updated 3.9 years ago by ▴ 360 • written 3.9 years ago by ▴ 10
1
vote
1
reply
1.4k
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News: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview pathways SBGNview.data pathview visualization
3.9 years ago Luo Weijun ★ 1.6k
2
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0
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1.2k
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
4.0 years ago Ben ▴ 50
2
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2
replies
1.4k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.2 years ago by 67k • written 4.2 years ago by • 0
2
votes
1
reply
2.8k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.6 years ago by ★ 3.4k • written 4.6 years ago by ▴ 50
0
votes
1
reply
2.2k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.8 years ago by 25k • written 4.8 years ago by • 0
0
votes
4
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1.3k
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Fonction of genes/metabolites in a pathway?
gene metabolite functionnal annotation pathways
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
0
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0
replies
1000
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.9 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
1.2k
views
Help for Research Proposal
drug development pathways bioinformatics
updated 6.2 years ago by ★ 13k • written 6.2 years ago by • 0
0
votes
0
replies
1.1k
views
Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
6.3 years ago anc.informatics • 0
0
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0
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799
views
Interactive metabolic pathway
pathways
6.5 years ago pritim2k6 • 0
0
votes
1
reply
1.2k
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
6.5 years ago ረ • 0
0
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0
replies
939
views
Could not find pathways in HSA gmt
pathways gmt
6.7 years ago flalix • 0
0
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5
replies
6.8k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 2.3 years ago by • 0 • written 6.7 years ago by ▴ 20
2
votes
4
replies
2.7k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 6.7 years ago by ★ 1.2k • written 6.7 years ago by • 0
0
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0
replies
1.3k
views
Pathview web - unable to map transcriptomic data
pathways high-throughput transcriptomics nonmodel species
6.8 years ago monteiro • 0
0
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0
replies
1.2k
views
igraph PoTRA error
graph pathways igraph
6.9 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 7.0 years ago by • 0 • written 11.3 years ago by ★ 1.6k
0
votes
0
replies
1.4k
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Two questions about pathifier package
pathways statistics microarray
7.1 years ago arronar • 0
1
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0
replies
1.6k
views
Job: Bioinformatician/Computational Biologist - Dublin City, Ireland
bioinformatician job computational biology genomes pathways machine learning Job
7.3 years ago bulfin.triona ▴ 10
0
votes
1
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2.2k
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GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 7.8 years ago by ★ 1.6k • written 7.8 years ago by • 0
0
votes
1
reply
2.4k
views
Pathview: visualization of data
pathways
updated 7.9 years ago by ★ 1.6k • written 7.9 years ago by • 0
0
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0
replies
1.4k
views
Pathway analysis for diffrential express gene
pathways gage annotation gostats
7.9 years ago avinash gupta ▴ 130
0
votes
0
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1.5k
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Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job phd R pathways Job
8.1 years ago Frank Kramer ▴ 60
0
votes
6
replies
1.8k
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Is reactome.db still updated?
reactome.db annotation pathways
8.3 years ago Guido Hooiveld ★ 4.1k
0
votes
4
replies
2.2k
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 8.4 years ago by ▴ 40 • written 8.4 years ago by • 0
2
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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
8.4 years ago Frank Kramer ▴ 60
0
votes
2
replies
3.0k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
9.1 years ago hywel.williams • 0
2
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3
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5.4k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 3.5 years ago by • 0 • written 9.1 years ago by ▴ 20
2
votes
1
reply
1.3k
views
Problem with data not found using pathview package
pathways
updated 9.7 years ago by 67k • written 9.7 years ago by • 0
8
votes
14
replies
4.4k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 9.8 years ago by ▴ 150 • written 10.2 years ago by ★ 1.2k
1
vote
15
replies
4.0k
views
reactome.db: reactome IDs not mapped to pathway names
annotation pathways
updated 9.8 years ago by ▴ 150 • written 10.3 years ago by ★ 2.1k
0
votes
2
replies
2.0k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 9.9 years ago by ★ 1.6k • written 9.9 years ago by ▴ 100
0
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13
replies
6.5k
views
gage pathways enrichment analysis
gage pathways kegg
updated 10.2 years ago by ★ 1.6k • written 10.2 years ago by ▴ 100
0
votes
2
replies
4.9k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 10.2 years ago by ★ 1.6k • written 10.2 years ago by ▴ 100
0
votes
0
replies
2.5k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
10.4 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.9k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
10.4 years ago Guest User ★ 13k
0
votes
0
replies
1.7k
views
Error in keggPathwayGraphs when updateCache = TRUE
Pathways ROntoTools Pathways ROntoTools
10.5 years ago Guest User ★ 13k
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by jodan • 0
Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…
Answer: Unused arguments error without used arguments in GSVA? by jodan • 0
It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and max…
Answer: Using genomicRanges / plyranges to calculate score of peaks within intervals by Michael Love 43k
This should be possible with plyranges using `join_overlap` and `group_by` on the metadata from the tile. E.g. create `tile.id` as a variab…
Answer: Reducing and aggregating GRanges with gaps using plyranges by Michael Love 43k
I added `min.gapwidth` to `reduce_ranges()` in recent plyranges releases: https://github.com/tidyomics/plyranges/pull/105
Answer: Find exact GRanges match keeping metadata columns by Michael Love 43k
You could use `minoverlap` but that requires an integer, not a fraction: ``` gr1 |> join_overlap_left(gr2, minoverlap=6) ``` Plyranges do…
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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