Showing : gage • reset
0
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13
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5.8k
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gage pathways enrichment analysis
gage pathways kegg
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 100
2
votes
11
replies
4.5k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
6.8 years ago Luo Weijun ★ 1.6k
0
votes
4
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2.2k
views
GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
gage pathview
8.6 years ago martin.hoelzer ▴ 20
1
vote
4
replies
2.3k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 7.4 years ago by ★ 1.2k • written 7.7 years ago by ▴ 110
0
votes
9
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3.1k
views
Urgent: Do GAGE applicable for non model species?
gage
updated 8.8 years ago by • 0 • written 8.8 years ago by ▴ 10
0
votes
13
replies
2.1k
views
Gage and setp argument
gsea gage
8.0 years ago • updated 7.9 years ago peter.chernek • 0
4
votes
4
replies
7.8k
views
Packages for GO and KEGG analysis on RNAseq data
GO gage goseq KEGG
updated 9.5 years ago by 50k • written 9.6 years ago by ▴ 120
6
votes
5
replies
1.5k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.1 years ago by ★ 1.6k • written 3.1 years ago by • 0
0
votes
6
replies
3.5k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage pathview error
updated 7.8 years ago by ★ 1.6k • written 7.9 years ago by • 0
0
votes
2
replies
1.7k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 9.2 years ago by ★ 1.6k • written 9.2 years ago by ▴ 100
1
vote
3
replies
1.5k
views
DESeq2 rlog as input for GAGE
deseq2 gage
7.8 years ago Tom ▴ 10
0
votes
4
replies
2.0k
views
Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
7.3 years ago bioinf ▴ 10
1
vote
3
replies
1.6k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
8.2 years ago serpalma.v ▴ 60
0
votes
2
replies
1.6k
views
Error when installing package gageData
gage kegg
6.2 years ago colaneri ▴ 30
3
votes
13
replies
2.5k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 14 months ago nute11a ▴ 10
0
votes
3
replies
1.9k
views
How to produce a dataframe with unique ENTREZID to use in gage?
gage annotationdbi entrez ensembl
6.2 years ago colaneri ▴ 30
0
votes
2
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1.4k
views
New gage package: Generally Applicable Gene-set/Pathway Analysis
Sequencing Microarray Pathways GO Yeast gage Sequencing Microarray Pathways GO Yeast
13.5 years ago Luo Weijun ★ 1.6k
1
vote
3
replies
1.1k
views
Creating gene set data for yeast
GAGE gene set go.gsets
updated 3.7 years ago by ★ 1.6k • written 3.7 years ago by ▴ 10
0
votes
5
replies
2.3k
views
Rgraphviz installation issue
Rgraphviz gage Rgraphviz gage
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by ▴ 100
4
votes
5
replies
1.7k
views
GAGE after tximport
gage tximport
updated 6.5 years ago by ★ 1.6k • written 6.5 years ago by ▴ 230
0
votes
1
reply
1.5k
views
GAGE vs other GO analysis tools
Microarray Pathways GO gage Microarray Pathways GO gage
updated 12.3 years ago by ★ 1.6k • written 12.3 years ago by ▴ 240
0
votes
2
replies
1.7k
views
Questions about Pathview, maybe also gage
Pathview Gage R
updated 7.3 years ago by ▴ 10 • written 7.8 years ago by • 0
0
votes
1
reply
1.9k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 7.0 years ago by ★ 1.6k • written 7.0 years ago by • 0
0
votes
2
replies
948
views
How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files
gage gage
12.3 years ago Javerjung Sandhu ▴ 200
0
votes
4
replies
1.9k
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 7.6 years ago by ▴ 40 • written 7.6 years ago by • 0
0
votes
1
reply
1.1k
views
A error in GAGE analysis
gage gage
updated 12.0 years ago by ★ 1.6k • written 12.0 years ago by ▴ 200
0
votes
2
replies
982
views
A question about the gage package
Microarray probe gage Microarray probe gage
11.1 years ago He, Yiwen NIH/CIT ▴ 360
0
votes
3
replies
2.3k
views
How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files
Microarray GO Cancer Breast gage Microarray GO Cancer Breast gage
updated 12.3 years ago by ▴ 200 • written 12.3 years ago by ★ 6.8k
0
votes
1
reply
1.1k
views
gage package: biological replicates and technical replicates
gage gage
updated 13.4 years ago by ★ 1.6k • written 13.4 years ago by ▴ 360
0
votes
2
replies
1.6k
views
GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE pathview
updated 7.3 years ago by ★ 1.6k • written 7.4 years ago by ▴ 30
0
votes
2
replies
1.6k
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage gage package
updated 7.5 years ago by ★ 1.6k • written 7.5 years ago by • 0
0
votes
1
reply
1.2k
views
GAGE: no essential member genes for some DE pathways
gage
updated 6.9 years ago by ★ 1.6k • written 7.0 years ago by • 0
2
votes
5
replies
2.9k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 8.4 years ago by ★ 6.8k • written 8.4 years ago by ▴ 30
0
votes
1
reply
1.1k
views
GAGE Package: Problem with probeset IDs conversion to Gene names or vice versa
convert gage convert gage
updated 12.1 years ago by ★ 1.6k • written 12.2 years ago by ▴ 200
0
votes
2
replies
1.5k
views
GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE Cuffdiff gene names
updated 8.4 years ago by ★ 1.6k • written 8.4 years ago by ▴ 30
0
votes
1
reply
1.0k
views
gage package Re: gene set enrichment analysis with missing values
gage gage
updated 13.5 years ago by ★ 1.6k • written 13.5 years ago by ▴ 360
0
votes
1
reply
1.0k
views
GAGE Package: Problem with Affymetrix hg u133 plus 2 probeset IDs conversion to Gene names or vice versa
convert gage convert gage
12.2 years ago Javerjung Sandhu ▴ 200
0
votes
1
reply
1.3k
views
gage function---kegg.gsets
gage gage
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by ★ 13k
0
votes
6
replies
2.6k
views
Gene set enrichment analysis with gage package returning NaN p-values
gage gsea rnaseq
updated 9.0 years ago by ★ 1.6k • written 9.0 years ago by • 0
2
votes
2
replies
1.7k
views
Output from pathview does not seem to match input
pathview gage pathway analysis
updated 8.8 years ago by ★ 1.6k • written 8.8 years ago by • 0
0
votes
1
reply
1.7k
views
An. Gambie RNA-Seq differential expression using gage and pathview
Transcription Annotation Normalization gage pathview Transcription Annotation Normalization
updated 9.8 years ago by ▴ 20 • written 9.8 years ago by ★ 1.6k
0
votes
1
reply
1.5k
views
Can gage not use large gene sets for pathway analysis?
Pathways gage pathview Pathways gage pathview
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by ★ 13k
0
votes
1
reply
1.3k
views
GAGE: question about interpretation of "ambiguous" results from geneset analysis
Microarray Pathways Escherichia coli gage Microarray Pathways Escherichia coli gage
13.2 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
1.1k
views
GAGE analysis
Microarray gage Microarray gage
updated 10.3 years ago by ★ 1.6k • written 10.3 years ago by ▴ 130
0
votes
1
reply
2.4k
views
gage and GO analysis
GO convert gage GO convert gage
updated 10.3 years ago by ▴ 570 • written 10.3 years ago by ★ 13k
0
votes
3
replies
1.7k
views
GAGE and PATHVIEW packages
gage pathview gage pathview
updated 10.6 years ago by ★ 1.6k • written 10.6 years ago by ▴ 150
0
votes
1
reply
3.0k
views
GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
GO Visualization edgeR gage GO Visualization edgeR gage
10.6 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
985
views
Error in GAGE analysis, help URGENTLY required
gage gage
12.2 years ago Javerjung Sandhu ▴ 200
0
votes
1
reply
1.4k
views
Can GAGE be used for transcript set pathway analysis
Pathways gage Pathways gage
updated 10.0 years ago by ★ 1.6k • written 10.0 years ago by ▴ 100
0
votes
7
replies
4.7k
views
Simple pathway enrichment analysis for gene lists
Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools
updated 10.6 years ago by ▴ 470 • written 10.6 years ago by ▴ 660
50 results • Page 1 of 1
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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