Showing : pathways • reset
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BioPAX parsing
Pathways Network Rgraphviz rBiopaxParser Pathways Network Rgraphviz rBiopaxParser
13.2 years ago Frank Kramer ▴ 10
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KEGGSOAP: list.pathways(org) or alternative way
Pathways Organism KEGGSOAP Pathways Organism KEGGSOAP
updated 13.3 years ago by ★ 7.2k • written 13.3 years ago by ▴ 30
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total gene number for a given species in reactome.db
Pathways Pathways
updated 13.3 years ago by ★ 7.2k • written 13.3 years ago by ▴ 300
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BioPAX parsing
Pathways Visualization Network graph Pathways Visualization Network graph
13.4 years ago Oliver Ruebenacker ▴ 110
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3
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pathway ID in KEGG.db
Pathways cycle Pathways cycle
updated 13.4 years ago by ★ 7.2k • written 13.4 years ago by ▴ 230
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3
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Kegg pathways overlay with log fold change values
Pathways limma SPIA Pathways limma SPIA
updated 13.5 years ago by ▴ 120 • written 13.5 years ago by ▴ 50
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"graphite" Biocarta 'native' graphs different from Biocarta web site?
Transcription Pathways Leukemia graphite Transcription Pathways Leukemia graphite
13.5 years ago Hamid Bolouri ▴ 90
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BioPAX/SBPAX import for MicroArray Analysis and Hypothesis Building
Microarray Pathways Network Microarray Pathways Network
updated 13.5 years ago by ★ 4.2k • written 13.5 years ago by ▴ 110
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edge-less pathways in graphite
Pathways graph Pathways graph
13.6 years ago Paul Shannon ▴ 750
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Biological Pathway Database
Transcription Pathways Category Transcription Pathways Category
written 13.6 years ago by ▴ 10
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Affy data analysis
Pathways GO affy Pathways GO affy
updated 13.6 years ago by 68k • written 13.6 years ago by ▴ 180
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Affymetrix data
Normalization Pathways GO annotate Normalization Pathways GO annotate
updated 13.6 years ago by ▴ 200 • written 13.6 years ago by ▴ 180
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ChIPpeakAnno on pathway enrichment
Pathways GO ChIPpeakAnno Pathways GO ChIPpeakAnno
updated 13.7 years ago by ▴ 240 • written 13.7 years ago by ★ 4.3k
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question from any of TopGO, gage, sigpathway, GSVA, GOstat users
miRNA Pathways miRNA Pathways
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ▴ 290
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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 3.4 years ago by • 0 • written 13.8 years ago by ★ 7.2k
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miRNA- KEGG
Pathways Pathways
updated 13.8 years ago by ▴ 610 • written 13.8 years ago by ▴ 290
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Fwd: miRNA- KEGG
Pathways Pathways
13.8 years ago Vincent J. Carey, Jr. 6.7k
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GO Analysis for Mouse Exon Array
Annotation Pathways GO limma GOstats oligo Annotation Pathways GO limma GOstats oligo
updated 13.8 years ago by ★ 4.3k • written 13.8 years ago by ▴ 60
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Deferential gene expression databases
Microarray Genetics Annotation Normalization Pathways GO Cancer BSgenome probe annotate
13.8 years ago saikouy bah ▴ 30
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Problem using KEGGSOAP: multiple genes per identity
Pathways KEGGSOAP Pathways KEGGSOAP
13.8 years ago January Weiner ▴ 240
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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 13.9 years ago by ▴ 200 • written 13.9 years ago by 25k
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A bug in either KEGG or KEGGSOAP?
Pathways KEGGSOAP Pathways KEGGSOAP
updated 13.9 years ago by ★ 7.2k • written 13.9 years ago by ▴ 230
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1
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GAGE vs other GO analysis tools
Microarray Pathways GO gage Microarray Pathways GO gage
updated 13.9 years ago by ★ 1.6k • written 13.9 years ago by ▴ 240
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Bioconductor resources for immunology
Pathways GO SPIA Pathways GO SPIA
14.0 years ago January Weiner ▴ 240
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Job: Seeking a Postdoctoral Researcher or Research Associate , RIKEN Yokohama Institute, Japan
Annotation Pathways Annotation Pathways
14.0 years ago Dr. Sujatha Mohan ▴ 10
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SPIA package
Pathways Organism SPIA Pathways Organism SPIA
14.0 years ago Tarca, Adi ▴ 570
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question for SPIA package
Pathways SPIA Pathways SPIA
14.0 years ago Jing Huang ▴ 380
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1
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1.1k
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KEGGSOAP incomplete list.pathways
Pathways KEGGSOAP Pathways KEGGSOAP
updated 14.0 years ago by ★ 7.2k • written 14.0 years ago by ★ 13k
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Why are there different number of pathways in pathway2gene and in pathway2name (KEGG.db)?
Pathways Pathways
14.1 years ago Marc Carlson ★ 7.2k
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Why are there different number of pathways in pathway2gene and in pathway2name (KEGG.db)?
Pathways Pathways
14.1 years ago Peng Yu ▴ 950
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[Job] Functional genomic analysis of cancer/RNAi screening
Transcription Sequencing Genetics Pathways Cancer Prostate Transcription Sequencing Cancer
14.1 years ago Sean Davis 21k
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Postdoctoral Fellow - Bioinformatics - Singapore, IMCB, Biopolis
Genetics Metabolomics Pathways Cancer Genetics Metabolomics Pathways Cancer
14.2 years ago Emilie Bard ▴ 10
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question for you on SPIA package
Pathways Organism SPIA Pathways Organism SPIA
14.2 years ago Tarca, Adi ▴ 570
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GAGE package help required
Pathways gage Pathways gage
14.3 years ago Luo Weijun ★ 1.6k
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PhD student in Bioinformatics, Computational Biology at Technical University of Munich, Germany
Proteomics Pathways Proteomics Pathways
14.3 years ago Amin Moghaddasi ▴ 130
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1.1k
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Are bioconductor packages designed for enrichment analysis affected by KEGG privatization ?
Pathways GOstats Pathways GOstats
updated 14.3 years ago by ★ 7.2k • written 14.3 years ago by ▴ 240
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[Bioc-sig-seq] Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Survival
updated 14.6 years ago by ▴ 310 • written 14.6 years ago by ★ 8.2k
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Bioconductor 2.8 is released
SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Network
updated 14.6 years ago by ▴ 310 • written 14.6 years ago by ★ 8.2k
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GO enrichment and pathways
Pathways GO Pathways GO
updated 14.6 years ago by ▴ 240 • written 14.6 years ago by ▴ 240
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3.1k
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goseq KEGG testing?
Pathways GO PROcess Category goseq Pathways GO PROcess Category goseq
updated 14.7 years ago by ▴ 40 • written 14.7 years ago by ★ 2.0k
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1.9k
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Which resources for pathway analysis?
Pathways Network SPIA DEGraph Pathways Network SPIA DEGraph
updated 14.8 years ago by ▴ 370 • written 14.8 years ago by ▴ 100
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1.5k
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Which resources for pathway analysis?
Pathways SPIA Pathways SPIA
updated 14.8 years ago by ▴ 300 • written 14.8 years ago by ▴ 370
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NCI pathways to graphNEL
Pathways graph Rredland GeneAnswers Pathways graph Rredland GeneAnswers
14.8 years ago laurent jacob ▴ 100
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1.5k
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GAGE: question about interpretation of "ambiguous" results from geneset analysis
Microarray Pathways Escherichia coli gage Microarray Pathways Escherichia coli gage
14.8 years ago Luo Weijun ★ 1.6k
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1.5k
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SPIA package with updated KEGG pathways
Pathways SPIA Pathways SPIA
updated 15.0 years ago by ★ 7.2k • written 15.0 years ago by ▴ 20
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Bioconductor Digest, Vol 94, Issue 10
Pathways SPIA Pathways SPIA
15.0 years ago Tarca, Adi ▴ 570
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3
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1.0k
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permutation
Pathways Pathways
updated 15.0 years ago by ★ 13k • written 15.0 years ago by ▴ 170
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5
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1.8k
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retrieve genes names after KEGG hypergeometric test
Annotation Pathways GO rat2302 probe affy Category Annotation Pathways GO rat2302 probe
updated 15.1 years ago by ▴ 930 • written 15.1 years ago by ▴ 230
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New gage package: Generally Applicable Gene-set/Pathway Analysis
Sequencing Microarray Pathways GO Yeast gage Sequencing Microarray Pathways GO Yeast
15.1 years ago Luo Weijun ★ 1.6k
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error in plotKEGGGraph
Pathways GLAD KEGGgraph Pathways GLAD KEGGgraph
15.2 years ago Robert M. Flight ▴ 280
246 results • Page 3 of 5
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Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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