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1
vote
1
reply
1.2k
views
Goseq output with too many GO terms per category
go goseq goterm category
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
0
votes
3
replies
2.2k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 6.8 years ago by ▴ 360 • written 6.8 years ago by ▴ 10
0
votes
4
replies
5.0k
views
goseq analysis - extracting list of my genes which are DE in the enriched GO category
GO Category goseq GO Category goseq
updated 8.0 years ago by ▴ 10 • written 12.6 years ago by ▴ 10
1
vote
0
replies
1.3k
views
enrichment analysis for gene pairs
go gostats category gsea
8.5 years ago Hector Corrada Bravo ▴ 60
0
votes
0
replies
1.3k
views
hyperGTest for MSigDB categories
category gostats msigdb hypergeometric test
8.7 years ago petyuk ▴ 70
0
votes
8
replies
2.0k
views
PFAM Enrichment in GOstats
PFAM Category GOstats
updated 8.9 years ago by ★ 1.2k • written 8.9 years ago by ▴ 930
2
votes
2
replies
1.1k
views
rownames for categoryReshape
Category
updated 9.4 years ago by 25k • written 9.4 years ago by • 0
1
vote
0
replies
1.2k
views
how to fetch GO categories from Chinese hamster genome
GO Category goseq
9.6 years ago upendra kumar devisetty ▴ 30
0
votes
1
reply
1.4k
views
GO enrichment
GO Category goseq GO Category goseq
9.7 years ago Guest User ★ 13k
0
votes
1
reply
1.6k
views
snpStats reference allele used in genetic associations?
SNP Category snpStats SNP Category snpStats
updated 9.9 years ago by 6.7k • written 9.9 years ago by ★ 13k
0
votes
0
replies
1.8k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
10.1 years ago Magda Price ▴ 60
0
votes
8
replies
4.8k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ★ 13k
0
votes
0
replies
2.0k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
10.2 years ago W. Evan Johnson ▴ 850
0
votes
0
replies
1.7k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
10.2 years ago Magda Price ▴ 60
0
votes
0
replies
1.7k
views
R pathview and mouse
Category pathview Category pathview
10.3 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
1.9k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription Annotation Normalization GO hgu133plus2 affy PROcess Category Transcription
updated 10.4 years ago by ▴ 80 • written 10.4 years ago by ▴ 20
0
votes
4
replies
3.6k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Annotation Normalization hgu133plus2 affy PROcess Category Annotation Normalization affy
updated 10.4 years ago by 65k • written 10.4 years ago by ★ 13k
0
votes
1
reply
1.0k
views
GSEABase error parsing msigdb_v4.0.xml
Category Category
updated 10.5 years ago by 25k • written 10.5 years ago by ▴ 10
0
votes
0
replies
1.3k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray limma Category CAMERA GSVA Microarray limma Category CAMERA GSVA
10.5 years ago Gordon Smyth 50k
0
votes
0
replies
1.1k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray Proteomics limma Category CAMERA GSVA Microarray Proteomics limma Category
10.5 years ago Pekka Kohonen ▴ 190
0
votes
1
reply
922
views
Which package I should use
Sequencing Category Sequencing Category
updated 10.6 years ago by ▴ 30 • written 10.6 years ago by ▴ 10
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
0
votes
1
reply
1.4k
views
topGO analysis returns different gene counts for category than given for non-model organism
GO Category topGO GO Category topGO
updated 10.6 years ago by ★ 6.8k • written 10.6 years ago by ▴ 20
0
votes
0
replies
1.3k
views
new window cairo bundle Re: [Rd] R/Sweave/cairo/freetype bug fix.
Category BEAT Category BEAT
10.9 years ago Hin-Tak Leung ▴ 30
0
votes
0
replies
1.0k
views
Diff Bind consultation
Category DiffBind Category DiffBind
11.0 years ago Rory Stark ★ 5.1k
0
votes
0
replies
1.0k
views
RE : ChIPpeakAnno_2.8.0 assignCromosomeRegion
annotate Category ChIPpeakAnno annotate Category ChIPpeakAnno
11.0 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
1.2k
views
[Rd] R/Sweave/cairo/freetype bug fix.
Category Category
updated 11.1 years ago by ▴ 60 • written 11.1 years ago by ▴ 30
0
votes
6
replies
1.1k
views
Extract microarray data for genes identified by GO analysis
Microarray GO Category Microarray GO Category
updated 11.2 years ago by 65k • written 11.2 years ago by ★ 13k
0
votes
2
replies
1.6k
views
GSEABase error parsing msigdb_v3.1.xml
GO Infrastructure hgu95av2 Biobase annotate graph Category AnnotationDbi BiocGenerics GO
updated 11.2 years ago by 25k • written 11.2 years ago by ▴ 80
0
votes
2
replies
1.2k
views
Difficulties in using the mgsa package for Gene Set Analysis
GO rat2302 Category mgsa GO rat2302 Category mgsa
updated 11.3 years ago by ▴ 60 • written 11.3 years ago by ★ 13k
0
votes
0
replies
803
views
ChIPpeakAnno
Annotation Category ChIPpeakAnno Annotation Category ChIPpeakAnno
11.4 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
896
views
HyperGTest 'count' value
Annotation Category Annotation Category
11.4 years ago Mary Kindall ▴ 70
0
votes
0
replies
696
views
strange results with edgeR::goodTuring
Category edgeR Category edgeR
11.6 years ago Gordon Smyth 50k
0
votes
2
replies
953
views
strange results with edgeR::goodTuring
Category edgeR Category edgeR
updated 11.6 years ago by 50k • written 11.6 years ago by ▴ 80
0
votes
3
replies
2.0k
views
oligo and pd.aragene.1.1.st annotation
Annotation limma Category pdInfoBuilder Annotation limma Category pdInfoBuilder
updated 11.7 years ago by ★ 7.2k • written 11.7 years ago by ▴ 20
0
votes
2
replies
1.0k
views
easyRNAseq question
Category DESeq easyRNASeq Category DESeq easyRNASeq
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ▴ 190
0
votes
3
replies
1.3k
views
GOstats - internal filtering?
Annotation GO hgu133plus2 GOstats Category Annotation GO hgu133plus2 GOstats Category
updated 12.0 years ago by 65k • written 12.0 years ago by ▴ 120
0
votes
0
replies
1.1k
views
Biological Pathway Database
Transcription Pathways Category Transcription Pathways Category
12.0 years ago Gita Singh ▴ 10
0
votes
3
replies
1.9k
views
Affymetrix Intronic Normalization Control Probes Differentially Expressed?
probe limma Category probe limma Category
updated 12.1 years ago by 65k • written 12.1 years ago by ▴ 10
0
votes
0
replies
1.2k
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer Apis mellifera BSgenome Biostrings Category BSgenome rtracklayer GO
12.1 years ago Matthew Young ▴ 50
1
vote
0
replies
2.1k
views
TopGO p-values VS DAVID p-values
Microarray GO Category topGO Microarray GO Category topGO
12.2 years ago Paul Geeleher ★ 1.3k
0
votes
1
reply
1.6k
views
PFAM gene enrichment test using GOstats and Category
SNP Annotation GO Organism affy GOstats Category SNP Annotation GO Organism affy
updated 12.3 years ago by ▴ 350 • written 12.3 years ago by ▴ 10
0
votes
1
reply
2.3k
views
PFAM gene enrichment test using GOstats and Category
Annotation GO Organism GOstats Category Annotation GO Organism GOstats Category
updated 12.4 years ago by ★ 7.2k • written 12.4 years ago by ▴ 10
0
votes
2
replies
1.8k
views
retrieve the level for a GO category
GO Category GO Category
updated 12.4 years ago by 25k • written 12.4 years ago by ▴ 150
0
votes
9
replies
1.6k
views
problem with GO terms
GO GOstats Category GO GOstats Category
updated 12.4 years ago by 65k • written 12.4 years ago by ▴ 620
0
votes
0
replies
1.1k
views
goSeq error (steve Shen)
GO Category edgeR goseq GO Category edgeR goseq
12.5 years ago Alicia Oshlack ▴ 100
0
votes
4
replies
1.9k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
limma Category edgeR limma Category edgeR
updated 12.5 years ago by ▴ 30 • written 12.5 years ago by 50k
0
votes
0
replies
1.1k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
Category edgeR Category edgeR
12.5 years ago Emanuel Heitlinger ▴ 30
0
votes
2
replies
2.2k
views
RNA seq analysis of Arabidopsis genome
GO Category goseq GO Category goseq
updated 12.6 years ago by ▴ 50 • written 12.6 years ago by ▴ 10
0
votes
0
replies
1.5k
views
I: R: R: R: Probe-level analysis of exon arrays using xps
Annotation Normalization Preprocessing Breast Prostate probe GLAD Category xps Annotation
12.6 years ago Lavorgna Giovanni ▴ 80
50 results • Page 1 of 1
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Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by sredemption • 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
Votes
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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