Showing : pathways • reset
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13
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4.6k
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gage pathways enrichment analysis
gage pathways kegg
updated 7.5 years ago by ★ 1.5k • written 7.5 years ago by ▴ 80
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2
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3.6k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 7.5 years ago by ★ 1.5k • written 7.5 years ago by ▴ 80
1
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3
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3.1k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 10 months ago by • 0 • written 6.4 years ago by ▴ 10
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4
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3.0k
views
clusterProfiler: exclude pathways and add gene names to cnetplot
clusterprofiler pathway analysis pathways
updated 4.0 years ago by ★ 1.2k • written 4.0 years ago by ▴ 20
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2.6k
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Pathview+GAGE workflow on RNA-seq data pathway analysis and visualization (was: Pathview published in Bioinformatics)
Annotation Pathways Visualization graph PROcess gage pathview Annotation Pathways graph
8.8 years ago Luo Weijun ★ 1.5k
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ComBat
Transcription Genetics Pathways Network Survival Cancer Breast Colon Kidney Leukemia HIV
9.6 years ago SSc Array Core ▴ 10
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0
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2.6k
views
DESeq2 with GAGE
Pathways cycle gage DESeq2 pathview Pathways cycle gage DESeq2 pathview
8.5 years ago Luo Weijun ★ 1.5k
8
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14
replies
2.6k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 7.1 years ago by ▴ 150 • written 7.5 years ago by ★ 1.2k
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6
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2.6k
views
LogFC query in Limma
Pathways convert Pathways convert
updated 9.3 years ago by 13k • written 9.3 years ago by ▴ 130
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0
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2.5k
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PhD student in Bioinformatics, Computational Biology at Technical University of Munich, Germany
Proteomics Pathways Proteomics Pathways
10.8 years ago Amin Moghaddasi ▴ 130
0
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4
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2.5k
views
Pathview for global and overview maps Re: using pathview about hsa01100
Pathways graph PROcess SIM gage pathview Pathways graph PROcess SIM gage pathview
updated 8.8 years ago by ▴ 230 • written 8.8 years ago by ★ 1.5k
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0
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2.3k
views
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 4 elements
Pathways Pathways
9.1 years ago Dario Strbenac ★ 1.5k
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5
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2.3k
views
use of voom function with attract package
Pathways GO attract Pathways GO attract
updated 8.1 years ago by 45k • written 8.1 years ago by ★ 12k
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1
reply
2.2k
views
BIRD 2008
Genetics Pathways Cancer PROcess microRNA a4 Genetics Pathways Cancer PROcess microRNA
14.6 years ago • updated 14.5 years ago Prof. Roland Wagner ▴ 100
1
vote
15
replies
2.2k
views
reactome.db: reactome IDs not mapped to pathway names
annotation pathways
updated 7.1 years ago by ▴ 150 • written 7.5 years ago by ★ 1.9k
0
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0
replies
2.2k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
8.8 years ago Luo Weijun ★ 1.5k
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0
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2.2k
views
Job: Seeking a Postdoctoral Researcher or Research Associate , RIKEN Yokohama Institute, Japan
Annotation Pathways Annotation Pathways
10.5 years ago Dr. Sujatha Mohan ▴ 10
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0
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2.1k
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Postdoctoral Fellow - Bioinformatics - Singapore, IMCB, Biopolis
Genetics Metabolomics Pathways Cancer Genetics Metabolomics Pathways Cancer
10.7 years ago Emilie Bard ▴ 10
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1
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2.0k
views
goseq KEGG testing?
Pathways GO PROcess Category goseq Pathways GO PROcess Category goseq
updated 11.2 years ago by ▴ 40 • written 11.2 years ago by ★ 2.0k
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2
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2.0k
views
how to get gene list for given GO terms?
Pathways GO Cancer PROcess goTools genomes Pathways GO Cancer PROcess goTools genomes
updated 10.2 years ago by ★ 1.3k • written 10.2 years ago by ★ 7.2k
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3
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1.9k
views
Kegg pathways overlay with log fold change values
Pathways limma SPIA Pathways limma SPIA
updated 10.0 years ago by ▴ 120 • written 10.0 years ago by ▴ 50
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5
replies
1.9k
views
Help using ENSMUSG ids in GOstats
Microarray Pathways GOstats Microarray Pathways GOstats
updated 14.0 years ago by ★ 5.5k • written 14.0 years ago by ▴ 30
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2
replies
1.9k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
6.4 years ago hywel.williams • 0
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4
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1.8k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
updated 14 months ago by ▴ 270 • written 14 months ago by ▴ 10
1
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1
reply
1.8k
views
miRNA- KEGG
Pathways Pathways
updated 10.2 years ago by ▴ 610 • written 10.2 years ago by ▴ 290
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0
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1.8k
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Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
7.7 years ago Luo Weijun ★ 1.5k
0
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1
reply
1.7k
views
Pathview - Problem with PNG output
Pathways graph pathview Pathways graph pathview
updated 8.7 years ago by ★ 1.5k • written 8.7 years ago by ▴ 150
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11
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1.7k
views
"graphite" Biocarta 'native' graphs different from Biocarta web site?
Transcription Pathways Leukemia graphite Transcription Pathways Leukemia graphite
10.0 years ago Hamid Bolouri ▴ 90
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1
reply
1.7k
views
Bioconductor Digest, Vol 120, Issue 12
Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy
9.3 years ago Matthew Thornton ▴ 350
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3
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1.6k
views
Visualizing KEGG pathways
Pathways graph Pathways graph
updated 13.1 years ago by ▴ 400 • written 13.1 years ago by ★ 1.1k
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0
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1.6k
views
Post Doc position, Berlin Germany
Sequencing Microarray Proteomics Pathways Network Cancer Sequencing Microarray Proteomics
13.1 years ago Paul Hammer ▴ 220
0
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0
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1.6k
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GAGE/Pathview RNA-Seq Workflows: reference genome issue
Pathways pathview Pathways pathview
8.2 years ago Luo Weijun ★ 1.5k
0
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6
replies
1.6k
views
GOstats and KEGG
Pathways GO GOstats Pathways GO GOstats
updated 15.5 years ago by ★ 7.4k • written 15.6 years ago by ▴ 190
0
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0
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1.5k
views
Pathview with non-KEGG organisms?
Pathways Organism pathview Pathways Organism pathview
8.8 years ago Luo Weijun ★ 1.5k
0
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5
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1.5k
views
GSEA and Broad gene sets
Pathways GSEABase Pathways GSEABase
updated 14.5 years ago by ★ 1.2k • written 14.5 years ago by ▴ 30
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3
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1.4k
views
hyperGTest, KEGG
Annotation Pathways multtest siggenes RBGL GOstats Annotation Pathways multtest siggenes
updated 15.1 years ago by ★ 7.4k • written 15.1 years ago by ▴ 80
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5
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1.4k
views
pathview puzzle
Pathways pathview Pathways pathview
8.8 years ago Oleg Moskvin ▴ 60
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3
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1.4k
views
[Bioc-sig-seq] Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Survival
updated 11.1 years ago by ▴ 310 • written 11.1 years ago by ★ 8.2k
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1
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1.4k
views
FW: URGENT Help required: Getting this error with GAGE analysis, input files attached
Microarray Annotation Pathways GO Cancer Breast cycle gage Microarray Annotation GO
updated 10.3 years ago by ▴ 200 • written 10.3 years ago by 25k
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0
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1.3k
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Postdoc positions at the Cancer Research UK Cambridge Research Institute
SNP Genetics Pathways Cancer CGH microRNA SNP Genetics Pathways Cancer CGH microRNA
13.6 years ago Florian Markowetz ▴ 20
0
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0
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1.3k
views
Deferential gene expression databases
Microarray Genetics Annotation Normalization Pathways GO Cancer BSgenome probe annotate
10.3 years ago saikouy bah ▴ 30
0
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1
reply
1.3k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 5.1 years ago by ★ 1.5k • written 5.1 years ago by • 0
0
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0
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1.3k
views
BIRD 2008 Conference Call for papers
Genetics Pathways Cancer microRNA Genetics Pathways Cancer microRNA
14.4 years ago Prof. Roland Wagner ▴ 100
0
votes
3
replies
1.3k
views
plot QuSAGE problem
Pathways qusage Pathways qusage
updated 8.5 years ago by ▴ 20 • written 8.5 years ago by ★ 12k
0
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0
replies
1.2k
views
BIRD 2008 Conference
Genetics Pathways Cancer microRNA Genetics Pathways Cancer microRNA
14.4 years ago Prof. Roland Wagner ▴ 100
0
votes
3
replies
1.2k
views
runSPIA() in graphite package
Pathways Breast siggenes PROcess cycle graphite Pathways Breast siggenes PROcess cycle
updated 9.3 years ago by ▴ 20 • written 9.3 years ago by ▴ 420
0
votes
1
reply
1.2k
views
Pathview: visualization of data
pathways
updated 5.2 years ago by ★ 1.5k • written 5.2 years ago by • 0
0
votes
2
replies
1.2k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 7.2 years ago by ★ 1.5k • written 7.2 years ago by ▴ 80
2
votes
1
reply
1.2k
views
Pathview graph with multiple states/samples or time series
Pathways graph Pathways graph
updated 4.3 years ago by • 0 • written 8.6 years ago by ★ 1.5k
0
votes
4
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1.2k
views
KEGGgraph
Pathways Organism graph PROcess KEGGgraph Pathways Organism graph PROcess KEGGgraph
9.6 years ago Ricardo Silva ▴ 110
50 results • Page 1 of 1
Recent ...
Replies
Answer: regression analysis for epic array methylation data using limma by Basti ▴ 280
Which package do you intend to use ? There are many tutorials in packages vignette that show you how to perform differential methylation an…
Comment: scRNASeq reference at a transcript level by Basti ▴ 280
I believe this question is not related to any Bioconductor package, I think the only solution to this question is to search yourself in Pub…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Upgrading the package solved the issue, thanks!
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2 by ATpoint ★ 1.2k
The error comes from the `mixsqp` package, see https://github.com/stephens999/ashr/issues/131. Upgrading the package to the most recent 0.3…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Thanks for the suggestion. I ran the following filtering criteria: ``` keep <- rowSums(counts(dds) >= 10) >= 5 dds <- dds[keep,] ``` It ga…
Votes
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: UniprotKB AC/ID to Entrez ID Conversion
edgeR: what to do with no replicates
Differential gene expression anlaysis?
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