Showing : Pathways • reset
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Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
updated 4 months ago by ▴ 270 • written 4 months ago by ▴ 10
1
vote
1
reply
228
views
News: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview pathways SBGNview.data pathview visualization
4 months ago Luo Weijun ★ 1.5k
1
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0
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101
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Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
6 months ago Ben ▴ 20
2
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2
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215
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Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 7 months ago by 57k • written 7 months ago by • 0
2
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1
reply
294
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pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 12 months ago by ★ 2.7k • written 12 months ago by ▴ 40
0
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1
reply
131
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 15 months ago by 25k • written 15 months ago by • 0
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4
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179
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Fonction of genes/metabolites in a pathway?
gene metabolite functionnal annotation pathways
updated 16 months ago by 3.2k • written 16 months ago by • 0
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0
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125
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
16 months ago Assa Yeroslaviz ★ 1.5k
2
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2
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332
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Help for Research Proposal
drug development pathways bioinformatics
updated 2.6 years ago by 13k • written 2.6 years ago by • 0
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0
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387
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Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
2.8 years ago anc.informatics • 0
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0
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259
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Interactive metabolic pathway
pathways
2.9 years ago pritim2k6 • 0
0
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1
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396
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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
3.0 years ago ረ • 0
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0
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322
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Could not find pathways in HSA gmt
pathways gmt
3.1 years ago flalix • 0
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4
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2.1k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 3.2 years ago by ★ 1.2k • written 3.2 years ago by ▴ 20
2
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4
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778
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ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 3.2 years ago by ★ 1.2k • written 3.2 years ago by • 0
0
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0
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396
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Pathview web - unable to map transcriptomic data
pathways high-throughput transcriptomics nonmodel species
3.3 years ago monteiro • 0
0
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0
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412
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igraph PoTRA error
graph pathways igraph
3.4 years ago genomic8328 ▴ 10
2
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1
reply
1.0k
views
Pathview graph with multiple states/samples or time series
Pathways graph Pathways graph
updated 3.5 years ago by • 0 • written 7.8 years ago by ★ 1.5k
0
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0
replies
473
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Two questions about pathifier package
pathways statistics microarray
3.5 years ago arronar • 0
1
vote
0
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648
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Job: Bioinformatician/Computational Biologist - Dublin City, Ireland
bioinformatician job computational biology genomes pathways machine learning Job
3.8 years ago bulfin.triona ▴ 10
0
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1
reply
1.1k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 4.2 years ago by ★ 1.5k • written 4.2 years ago by • 0
0
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1
reply
980
views
Pathview: visualization of data
pathways
updated 4.4 years ago by ★ 1.5k • written 4.4 years ago by • 0
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0
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642
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Pathway analysis for diffrential express gene
pathways gage annotation gostats
4.4 years ago avinash gupta ▴ 130
0
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0
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718
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Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job phd R pathways Job
4.6 years ago Frank Kramer ▴ 60
0
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6
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640
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Is reactome.db still updated?
reactome.db annotation pathways
4.8 years ago Guido Hooiveld ★ 3.0k
0
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4
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933
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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 4.8 years ago by ▴ 40 • written 4.8 years ago by • 0
2
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0
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839
views
Job: PhD student positions in the areas of Bioinformatics, Computer Science and Biostatistics
bioinformatician job job phd R pathways Job
4.9 years ago Frank Kramer ▴ 60
0
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2
replies
1.7k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
5.5 years ago hywel.williams • 0
1
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3
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2.7k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 6 days ago by • 0 • written 5.6 years ago by ▴ 10
2
votes
1
reply
682
views
Problem with data not found using pathview package
pathways
updated 6.2 years ago by 57k • written 6.2 years ago by • 0
8
votes
14
replies
2.3k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 6.3 years ago by ▴ 150 • written 6.7 years ago by ★ 1.2k
1
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15
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1.9k
views
reactome.db: reactome IDs not mapped to pathway names
annotation pathways
updated 6.3 years ago by ▴ 150 • written 6.7 years ago by ★ 1.9k
0
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2
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1.1k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 6.4 years ago by ★ 1.5k • written 6.4 years ago by ▴ 60
0
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13
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4.3k
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gage pathways enrichment analysis
gage pathways kegg
updated 6.7 years ago by ★ 1.5k • written 6.7 years ago by ▴ 60
0
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2
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3.3k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 6.7 years ago by ★ 1.5k • written 6.7 years ago by ▴ 60
0
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0
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1.6k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
6.9 years ago Luo Weijun ★ 1.5k
0
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0
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1.1k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
6.9 years ago Guest User ★ 12k
0
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0
replies
953
views
Error in keggPathwayGraphs when updateCache = TRUE
Pathways ROntoTools Pathways ROntoTools
7.0 years ago Guest User ★ 12k
0
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0
replies
803
views
ISMB talks: Pathview for pathway-based data integration and visualization
Pathways Visualization pathview Pathways Visualization pathview
7.1 years ago Luo Weijun ★ 1.5k
0
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0
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616
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ECCB 2014
Sequencing Pathways Sequencing Pathways
7.2 years ago Wolfgang Raffelsberger ▴ 60
0
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0
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857
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PostDoc opportunity
Pathways Network Pathways Network
7.2 years ago Guest User ★ 12k
0
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0
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568
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Thalassiosira pseudonana
Annotation Pathways GO Annotation Pathways GO
7.2 years ago nooshin ▴ 290
0
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0
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622
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graphite biopax conversion code?
Pathways graphite Pathways graphite
7.2 years ago Ryan C. Thompson 7.6k
0
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1
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890
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Can GAGE be used for transcript set pathway analysis
Pathways gage Pathways gage
updated 7.2 years ago by ★ 1.5k • written 7.2 years ago by ▴ 100
0
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5
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1.9k
views
use of voom function with attract package
Pathways GO attract Pathways GO attract
updated 7.3 years ago by 43k • written 7.3 years ago by ★ 12k
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0
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805
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KEGG pathway analysis with ReportingTools
Pathways GO ReportingTools Pathways GO ReportingTools
7.3 years ago Mayte Suarez-Farinas ▴ 510
0
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0
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1.0k
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[phenoTest package]: gsea.kegg error with absVals parameter
Pathways GO hgu133a hgu95av2 phenoTest Pathways GO hgu133a hgu95av2 phenoTest
7.3 years ago Kostas Kerkentzes ▴ 10
0
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0
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1.0k
views
pathview with tomato and minor species
Pathways pathview Pathways pathview
7.4 years ago Luo Weijun ★ 1.5k
0
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0
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1.5k
views
GAGE/Pathview RNA-Seq Workflows: reference genome issue
Pathways pathview Pathways pathview
7.4 years ago Luo Weijun ★ 1.5k
0
votes
1
reply
726
views
SPIA
Pathways SPIA Pathways SPIA
updated 7.4 years ago by ▴ 570 • written 7.4 years ago by ★ 12k
50 results • Page 1 of 1
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Answer: How to extract DEG from limmarResults object after beadarray analysis by Gordon Smyth 43k
I am the limma package author, but I don't know how to help you. The beadarray package has done a standard limma analysis but, instead of s…
Comment: An error using Diffbind plotprofile by doug.barrows • 0
Hi there, it's hard to tell how to debug without having the data. Could you potentially send me the object you are attempting to use for th…
Comment: DESeq2 Shrinkage methods for scRNA-Seq by Pedro Tan • 0
Thanks Michael! I will stick to apeglm and incorporate alternate size factors for single cell data. All the best, Pedro
Answer: Macbook M1 install genefilter failed by soda ▴ 10
i have solved this problem by myself. share with you. you need to download gfortran in path /opt/R/arm64/bin this website helped me: **h…
Comment: Best practice for quantifying sncRNA by James W. MacDonald 57k
If you used the QIASeq miRNA library, then you are wasting your time. That library adds the UMI barcodes and is intended for you to then up…
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Answer: Macbook M1 install genefilter failed
BioCAsia Virtual Meeting, 15-18 October 2020
Answer: Selecting pairs of exons from differentially spliced genes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
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