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1
vote
1
reply
1.5k
views
Goseq output with too many GO terms per category
go goseq goterm category
updated 6.6 years ago by 52k • written 6.6 years ago by • 0
0
votes
3
replies
2.5k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 7.7 years ago by ▴ 370 • written 7.8 years ago by ▴ 10
0
votes
4
replies
5.4k
views
goseq analysis - extracting list of my genes which are DE in the enriched GO category
GO Category goseq GO Category goseq
updated 9.0 years ago by ▴ 10 • written 13.5 years ago by ▴ 10
1
vote
0
replies
1.6k
views
enrichment analysis for gene pairs
go gostats category gsea
9.4 years ago Hector Corrada Bravo ▴ 60
0
votes
0
replies
1.5k
views
hyperGTest for MSigDB categories
category gostats msigdb hypergeometric test
9.6 years ago petyuk ▴ 70
0
votes
8
replies
2.5k
views
PFAM Enrichment in GOstats
PFAM Category GOstats
updated 9.9 years ago by ★ 1.2k • written 9.9 years ago by ▴ 930
2
votes
2
replies
1.2k
views
rownames for categoryReshape
Category
updated 10.3 years ago by 25k • written 10.3 years ago by • 0
1
vote
0
replies
1.4k
views
how to fetch GO categories from Chinese hamster genome
GO Category goseq
10.5 years ago upendra kumar devisetty ▴ 30
0
votes
1
reply
1.6k
views
GO enrichment
GO Category goseq GO Category goseq
10.6 years ago Guest User ★ 13k
0
votes
1
reply
1.9k
views
snpStats reference allele used in genetic associations?
SNP Category snpStats SNP Category snpStats
updated 10.8 years ago by 6.7k • written 10.8 years ago by ★ 13k
0
votes
0
replies
2.0k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
11.0 years ago Magda Price ▴ 60
0
votes
8
replies
5.3k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
updated 11.0 years ago by ★ 13k • written 11.0 years ago by ★ 13k
0
votes
0
replies
2.2k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
11.1 years ago W. Evan Johnson ▴ 870
0
votes
0
replies
1.9k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
11.1 years ago Magda Price ▴ 60
0
votes
0
replies
1.9k
views
R pathview and mouse
Category pathview Category pathview
11.2 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
2.2k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription Annotation Normalization GO hgu133plus2 affy PROcess Category Transcription
updated 11.3 years ago by ▴ 80 • written 11.3 years ago by ▴ 20
0
votes
4
replies
4.2k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Annotation Normalization hgu133plus2 affy PROcess Category Annotation Normalization affy
updated 11.3 years ago by 68k • written 11.3 years ago by ★ 13k
0
votes
1
reply
1.2k
views
GSEABase error parsing msigdb_v4.0.xml
Category Category
updated 11.4 years ago by 25k • written 11.4 years ago by ▴ 10
0
votes
0
replies
1.5k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray limma Category CAMERA GSVA Microarray limma Category CAMERA GSVA
11.4 years ago Gordon Smyth 52k
0
votes
0
replies
1.3k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray Proteomics limma Category CAMERA GSVA Microarray Proteomics limma Category
11.4 years ago Pekka Kohonen ▴ 190
0
votes
1
reply
1.1k
views
Which package I should use
Sequencing Category Sequencing Category
updated 11.5 years ago by ▴ 30 • written 11.5 years ago by ▴ 10
0
votes
7
replies
5.2k
views
Simple pathway enrichment analysis for gene lists
Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools
updated 11.5 years ago by ▴ 470 • written 11.5 years ago by ▴ 680
0
votes
1
reply
1.6k
views
topGO analysis returns different gene counts for category than given for non-model organism
GO Category topGO GO Category topGO
updated 11.6 years ago by ★ 6.8k • written 11.6 years ago by ▴ 20
0
votes
0
replies
1.5k
views
new window cairo bundle Re: [Rd] R/Sweave/cairo/freetype bug fix.
Category BEAT Category BEAT
11.8 years ago Hin-Tak Leung ▴ 30
0
votes
0
replies
1.2k
views
Diff Bind consultation
Category DiffBind Category DiffBind
11.9 years ago Rory Stark ★ 5.2k
0
votes
0
replies
1.2k
views
RE : ChIPpeakAnno_2.8.0 assignCromosomeRegion
annotate Category ChIPpeakAnno annotate Category ChIPpeakAnno
11.9 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
1.4k
views
[Rd] R/Sweave/cairo/freetype bug fix.
Category Category
updated 12.0 years ago by ▴ 60 • written 12.0 years ago by ▴ 30
0
votes
6
replies
1.3k
views
Extract microarray data for genes identified by GO analysis
Microarray GO Category Microarray GO Category
updated 12.1 years ago by 68k • written 12.1 years ago by ★ 13k
0
votes
2
replies
1.9k
views
GSEABase error parsing msigdb_v3.1.xml
GO Infrastructure hgu95av2 Biobase annotate graph Category AnnotationDbi BiocGenerics GO
updated 12.2 years ago by 25k • written 12.1 years ago by ▴ 80
0
votes
2
replies
1.5k
views
Difficulties in using the mgsa package for Gene Set Analysis
GO rat2302 Category mgsa GO rat2302 Category mgsa
updated 12.2 years ago by ▴ 60 • written 12.2 years ago by ★ 13k
0
votes
0
replies
977
views
ChIPpeakAnno
Annotation Category ChIPpeakAnno Annotation Category ChIPpeakAnno
12.4 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
1.1k
views
HyperGTest 'count' value
Annotation Category Annotation Category
12.4 years ago Mary Kindall ▴ 70
0
votes
0
replies
829
views
strange results with edgeR::goodTuring
Category edgeR Category edgeR
12.6 years ago Gordon Smyth 52k
0
votes
2
replies
1.1k
views
strange results with edgeR::goodTuring
Category edgeR Category edgeR
updated 12.6 years ago by 52k • written 12.6 years ago by ▴ 80
0
votes
3
replies
2.2k
views
oligo and pd.aragene.1.1.st annotation
Annotation limma Category pdInfoBuilder Annotation limma Category pdInfoBuilder
updated 12.6 years ago by ★ 7.2k • written 12.6 years ago by ▴ 20
0
votes
2
replies
1.2k
views
easyRNAseq question
Category DESeq easyRNASeq Category DESeq easyRNASeq
updated 12.7 years ago by ★ 13k • written 12.7 years ago by ▴ 190
0
votes
3
replies
1.6k
views
GOstats - internal filtering?
Annotation GO hgu133plus2 GOstats Category Annotation GO hgu133plus2 GOstats Category
updated 12.9 years ago by 68k • written 12.9 years ago by ▴ 120
0
votes
0
replies
1.4k
views
Biological Pathway Database
Transcription Pathways Category Transcription Pathways Category
12.9 years ago Gita Singh ▴ 10
0
votes
3
replies
2.1k
views
Affymetrix Intronic Normalization Control Probes Differentially Expressed?
probe limma Category probe limma Category
updated 13.0 years ago by 68k • written 13.0 years ago by ▴ 10
0
votes
0
replies
1.4k
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer Apis mellifera BSgenome Biostrings Category BSgenome rtracklayer GO
13.0 years ago Matthew Young ▴ 50
1
vote
0
replies
2.4k
views
TopGO p-values VS DAVID p-values
Microarray GO Category topGO Microarray GO Category topGO
13.1 years ago Paul Geeleher ★ 1.3k
0
votes
1
reply
1.9k
views
PFAM gene enrichment test using GOstats and Category
SNP Annotation GO Organism affy GOstats Category SNP Annotation GO Organism affy
updated 13.2 years ago by ▴ 350 • written 13.2 years ago by ▴ 10
0
votes
1
reply
2.5k
views
PFAM gene enrichment test using GOstats and Category
Annotation GO Organism GOstats Category Annotation GO Organism GOstats Category
updated 13.3 years ago by ★ 7.2k • written 13.3 years ago by ▴ 10
0
votes
2
replies
2.0k
views
retrieve the level for a GO category
GO Category GO Category
updated 13.3 years ago by 25k • written 13.3 years ago by ▴ 150
0
votes
9
replies
2.1k
views
problem with GO terms
GO GOstats Category GO GOstats Category
updated 13.3 years ago by 68k • written 13.3 years ago by ▴ 620
0
votes
0
replies
1.3k
views
goSeq error (steve Shen)
GO Category edgeR goseq GO Category edgeR goseq
13.4 years ago Alicia Oshlack ▴ 100
0
votes
4
replies
2.2k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
limma Category edgeR limma Category edgeR
updated 13.4 years ago by ▴ 30 • written 13.4 years ago by 52k
0
votes
0
replies
1.3k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
Category edgeR Category edgeR
13.4 years ago Emanuel Heitlinger ▴ 30
0
votes
2
replies
2.4k
views
RNA seq analysis of Arabidopsis genome
GO Category goseq GO Category goseq
updated 13.5 years ago by ▴ 50 • written 13.5 years ago by ▴ 10
0
votes
0
replies
1.7k
views
I: R: R: R: Probe-level analysis of exon arrays using xps
Annotation Normalization Preprocessing Breast Prostate probe GLAD Category xps Annotation
13.5 years ago Lavorgna Giovanni ▴ 80
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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