Showing : Pathways • reset
1
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4
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pathview - multiple states
pathview Pathways KEGG
18 days ago • updated 17 days ago Philippine • 0
3
votes
1
reply
1.0k
views
Difference between enrichGO results and Enrichr website results
Pathways GO.db clusterProfiler
updated 5 months ago by ★ 4.1k • written 5 months ago by ▴ 10
1
vote
9
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1.5k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 6 months ago by 67k • written 6 months ago by ▴ 10
2
votes
3
replies
907
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
updated 5 weeks ago by • 0 • written 8 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 18.3 years ago by ▴ 30
0
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0
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609
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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
11 months ago omicsresearch • 0
0
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1
reply
693
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topGO() analysis of DMPs in missMethyl methylation analysis
DNAMethylation missMethyl Pathways
20 months ago Grace • 0
0
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0
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710
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Changing pathway names in pathway analysis
pathways Pathways
23 months ago Katharina • 0
0
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0
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835
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Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
2.1 years ago whduke • 0
0
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0
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988
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
2.7 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
2.8 years ago • updated 2.7 years ago m.glymenaki • 0
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6
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4.5k
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extracting the KEGG pathway for a set of genes
Pathways KEGG
3.4 years ago Bogdan ▴ 670
0
votes
4
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6.0k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
updated 3.7 years ago by ▴ 360 • written 3.7 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
3.8 years ago Luo Weijun ★ 1.6k
2
votes
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
3.9 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 4.0 years ago by 67k • written 4.0 years ago by • 0
2
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1
reply
2.7k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.4 years ago by ★ 3.4k • written 4.4 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 4.7 years ago by 25k • written 4.7 years ago by • 0
0
votes
4
replies
1.2k
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Fonction of genes/metabolites in a pathway?
gene metabolite functionnal annotation pathways
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by • 0
0
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0
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975
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.8 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
1.2k
views
Help for Research Proposal
drug development pathways bioinformatics
updated 6.0 years ago by ★ 13k • written 6.1 years ago by • 0
0
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0
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1.1k
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Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
6.2 years ago anc.informatics • 0
0
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0
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784
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Interactive metabolic pathway
pathways
6.3 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
6.4 years ago ረ • 0
0
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0
replies
912
views
Could not find pathways in HSA gmt
pathways gmt
6.5 years ago flalix • 0
0
votes
5
replies
6.7k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 2.2 years ago by • 0 • written 6.6 years ago by ▴ 20
2
votes
4
replies
2.6k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 6.6 years ago by ★ 1.2k • written 6.6 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
6.7 years ago monteiro • 0
0
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0
replies
1.1k
views
igraph PoTRA error
graph pathways igraph
6.8 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 6.9 years ago by • 0 • written 11.2 years ago by ★ 1.6k
0
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0
replies
1.4k
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Two questions about pathifier package
pathways statistics microarray
6.9 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
7.2 years ago bulfin.triona ▴ 10
0
votes
1
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2.1k
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GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 7.6 years ago by ★ 1.6k • written 7.6 years ago by • 0
0
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1
reply
2.3k
views
Pathview: visualization of data
pathways
updated 7.8 years ago by ★ 1.6k • written 7.8 years ago by • 0
0
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0
replies
1.4k
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Pathway analysis for diffrential express gene
pathways gage annotation gostats
7.8 years ago avinash gupta ▴ 130
0
votes
0
replies
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
8.0 years ago Frank Kramer ▴ 60
0
votes
6
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1.8k
views
Is reactome.db still updated?
reactome.db annotation pathways
8.2 years ago Guido Hooiveld ★ 4.1k
0
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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 8.2 years ago by ▴ 40 • written 8.2 years ago by • 0
2
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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
8.3 years ago Frank Kramer ▴ 60
0
votes
2
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3.0k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
8.9 years ago hywel.williams • 0
2
votes
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 3.4 years ago by • 0 • written 9.0 years ago by ▴ 20
2
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1
reply
1.3k
views
Problem with data not found using pathview package
pathways
updated 9.6 years ago by 67k • written 9.6 years ago by • 0
8
votes
14
replies
4.3k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 9.7 years ago by ▴ 150 • written 10.1 years ago by ★ 1.2k
1
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15
replies
4.0k
views
reactome.db: reactome IDs not mapped to pathway names
annotation pathways
updated 9.7 years ago by ▴ 150 • written 10.1 years ago by ★ 2.1k
0
votes
2
replies
2.0k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 9.8 years ago by ★ 1.6k • written 9.8 years ago by ▴ 100
0
votes
13
replies
6.4k
views
gage pathways enrichment analysis
gage pathways kegg
updated 10.1 years ago by ★ 1.6k • written 10.1 years ago by ▴ 100
0
votes
2
replies
4.9k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 10.1 years ago by ★ 1.6k • written 10.1 years ago by ▴ 100
0
votes
0
replies
2.5k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
10.3 years ago Luo Weijun ★ 1.6k
0
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0
replies
1.9k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
10.3 years ago Guest User ★ 13k
0
votes
0
replies
1.7k
views
Error in keggPathwayGraphs when updateCache = TRUE
Pathways ROntoTools Pathways ROntoTools
10.4 years ago Guest User ★ 13k
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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