Showing : Category • reset
1
vote
1
reply
840
views
Goseq output with too many GO terms per category
go goseq goterm category
updated 4.8 years ago by 47k • written 4.8 years ago by • 0
0
votes
3
replies
1.9k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 5.9 years ago by ▴ 360 • written 6.0 years ago by ▴ 10
0
votes
4
replies
4.6k
views
goseq analysis - extracting list of my genes which are DE in the enriched GO category
GO Category goseq GO Category goseq
updated 7.2 years ago by ▴ 10 • written 11.7 years ago by ▴ 10
1
vote
0
replies
1.1k
views
enrichment analysis for gene pairs
go gostats category gsea
7.6 years ago Hector Corrada Bravo ▴ 60
0
votes
0
replies
1.0k
views
hyperGTest for MSigDB categories
category gostats msigdb hypergeometric test
7.8 years ago petyuk ▴ 70
0
votes
8
replies
1.7k
views
PFAM Enrichment in GOstats
PFAM Category GOstats
updated 8.1 years ago by ★ 1.2k • written 8.1 years ago by ▴ 930
2
votes
2
replies
849
views
rownames for categoryReshape
Category
updated 8.5 years ago by 25k • written 8.5 years ago by • 0
1
vote
0
replies
968
views
how to fetch GO categories from Chinese hamster genome
GO Category goseq
8.7 years ago upendra kumar devisetty ▴ 30
0
votes
1
reply
1.1k
views
GO enrichment
GO Category goseq GO Category goseq
8.8 years ago Guest User ★ 12k
0
votes
1
reply
1.3k
views
snpStats reference allele used in genetic associations?
SNP Category snpStats SNP Category snpStats
updated 9.0 years ago by 6.6k • written 9.0 years ago by ★ 12k
0
votes
0
replies
1.6k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
9.2 years ago Magda Price ▴ 60
0
votes
8
replies
4.3k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
updated 9.2 years ago by 13k • written 9.2 years ago by ★ 12k
0
votes
0
replies
1.8k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
9.3 years ago W. Evan Johnson ▴ 840
0
votes
0
replies
1.5k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO Category sva GO Category sva
9.3 years ago Magda Price ▴ 60
0
votes
0
replies
1.5k
views
R pathview and mouse
Category pathview Category pathview
9.4 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
1.7k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription Annotation Normalization GO hgu133plus2 affy PROcess Category Transcription
updated 9.5 years ago by ▴ 80 • written 9.5 years ago by ▴ 20
0
votes
4
replies
3.3k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Annotation Normalization hgu133plus2 affy PROcess Category Annotation Normalization affy
updated 9.5 years ago by 63k • written 9.5 years ago by ★ 12k
0
votes
1
reply
852
views
GSEABase error parsing msigdb_v4.0.xml
Category Category
updated 9.6 years ago by 25k • written 9.6 years ago by ▴ 10
0
votes
0
replies
1.1k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray limma Category CAMERA GSVA Microarray limma Category CAMERA GSVA
9.6 years ago Gordon Smyth 47k
0
votes
0
replies
934
views
enrichment packages that accept t-stat (or related stat) as input
Microarray Proteomics limma Category CAMERA GSVA Microarray Proteomics limma Category
9.6 years ago Pekka Kohonen ▴ 190
0
votes
1
reply
733
views
Which package I should use
Sequencing Category Sequencing Category
updated 9.7 years ago by ▴ 30 • written 9.7 years ago by ▴ 10
0
votes
7
replies
4.2k
views
Simple pathway enrichment analysis for gene lists
Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools
updated 9.7 years ago by ▴ 470 • written 9.7 years ago by ▴ 660
0
votes
1
reply
1.2k
views
topGO analysis returns different gene counts for category than given for non-model organism
GO Category topGO GO Category topGO
updated 9.8 years ago by ★ 6.8k • written 9.8 years ago by ▴ 20
0
votes
0
replies
1.1k
views
new window cairo bundle Re: [Rd] R/Sweave/cairo/freetype bug fix.
Category BEAT Category BEAT
10.0 years ago Hin-Tak Leung ▴ 30
0
votes
0
replies
850
views
Diff Bind consultation
Category DiffBind Category DiffBind
10.1 years ago Rory Stark ★ 4.9k
0
votes
0
replies
824
views
RE : ChIPpeakAnno_2.8.0 assignCromosomeRegion
annotate Category ChIPpeakAnno annotate Category ChIPpeakAnno
10.1 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
928
views
[Rd] R/Sweave/cairo/freetype bug fix.
Category Category
updated 10.2 years ago by ▴ 60 • written 10.2 years ago by ▴ 30
0
votes
6
replies
839
views
Extract microarray data for genes identified by GO analysis
Microarray GO Category Microarray GO Category
updated 10.3 years ago by 63k • written 10.3 years ago by ★ 12k
0
votes
2
replies
1.3k
views
GSEABase error parsing msigdb_v3.1.xml
GO Infrastructure hgu95av2 Biobase annotate graph Category AnnotationDbi BiocGenerics GO
updated 10.3 years ago by 25k • written 10.3 years ago by ▴ 80
0
votes
2
replies
1.0k
views
Difficulties in using the mgsa package for Gene Set Analysis
GO rat2302 Category mgsa GO rat2302 Category mgsa
updated 10.4 years ago by ▴ 60 • written 10.4 years ago by ★ 12k
0
votes
0
replies
626
views
ChIPpeakAnno
Annotation Category ChIPpeakAnno Annotation Category ChIPpeakAnno
10.6 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
672
views
HyperGTest 'count' value
Annotation Category Annotation Category
10.6 years ago Mary Kindall ▴ 70
0
votes
0
replies
563
views
strange results with edgeR::goodTuring
Category edgeR Category edgeR
10.7 years ago Gordon Smyth 47k
0
votes
2
replies
746
views
strange results with edgeR::goodTuring
Category edgeR Category edgeR
updated 10.8 years ago by 47k • written 10.8 years ago by ▴ 80
0
votes
3
replies
1.6k
views
oligo and pd.aragene.1.1.st annotation
Annotation limma Category pdInfoBuilder Annotation limma Category pdInfoBuilder
updated 10.8 years ago by ★ 7.2k • written 10.8 years ago by ▴ 20
0
votes
2
replies
752
views
easyRNAseq question
Category DESeq easyRNASeq Category DESeq easyRNASeq
updated 10.9 years ago by 13k • written 10.9 years ago by ▴ 190
0
votes
3
replies
1.1k
views
GOstats - internal filtering?
Annotation GO hgu133plus2 GOstats Category Annotation GO hgu133plus2 GOstats Category
updated 11.1 years ago by 63k • written 11.1 years ago by ▴ 120
0
votes
0
replies
899
views
Biological Pathway Database
Transcription Pathways Category Transcription Pathways Category
11.1 years ago Gita Singh ▴ 10
0
votes
3
replies
1.6k
views
Affymetrix Intronic Normalization Control Probes Differentially Expressed?
probe limma Category probe limma Category
updated 11.2 years ago by 63k • written 11.2 years ago by ▴ 10
0
votes
0
replies
978
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer Apis mellifera BSgenome Biostrings Category BSgenome rtracklayer GO
11.2 years ago Matthew Young ▴ 50
1
vote
0
replies
1.9k
views
TopGO p-values VS DAVID p-values
Microarray GO Category topGO Microarray GO Category topGO
11.3 years ago Paul Geeleher ★ 1.3k
0
votes
1
reply
1.3k
views
PFAM gene enrichment test using GOstats and Category
SNP Annotation GO Organism affy GOstats Category SNP Annotation GO Organism affy
updated 11.4 years ago by ▴ 350 • written 11.4 years ago by ▴ 10
0
votes
1
reply
2.1k
views
PFAM gene enrichment test using GOstats and Category
Annotation GO Organism GOstats Category Annotation GO Organism GOstats Category
updated 11.5 years ago by ★ 7.2k • written 11.5 years ago by ▴ 10
0
votes
2
replies
1.6k
views
retrieve the level for a GO category
GO Category GO Category
updated 11.5 years ago by 25k • written 11.5 years ago by ▴ 150
0
votes
9
replies
1.2k
views
problem with GO terms
GO GOstats Category GO GOstats Category
updated 11.5 years ago by 63k • written 11.5 years ago by ▴ 620
0
votes
0
replies
903
views
goSeq error (steve Shen)
GO Category edgeR goseq GO Category edgeR goseq
11.6 years ago Alicia Oshlack ▴ 100
0
votes
4
replies
1.7k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
limma Category edgeR limma Category edgeR
updated 11.6 years ago by ▴ 30 • written 11.6 years ago by 47k
0
votes
0
replies
984
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
Category edgeR Category edgeR
11.6 years ago Emanuel Heitlinger ▴ 30
0
votes
2
replies
1.9k
views
RNA seq analysis of Arabidopsis genome
GO Category goseq GO Category goseq
updated 11.7 years ago by ▴ 50 • written 11.7 years ago by ▴ 10
0
votes
0
replies
1.2k
views
I: R: R: R: Probe-level analysis of exon arrays using xps
Annotation Normalization Preprocessing Breast Prostate probe GLAD Category xps Annotation
11.7 years ago Lavorgna Giovanni ▴ 80
50 results • Page 1 of 1
Recent ...
Replies
Answer: Extract Limma Adjusted Values for Plotting by James W. MacDonald 63k
You should use `removeBatchEffect` for that.
Comment: Interpret plot from DiffBind by Chris • 0
Thank you for the explanation! The purple (**gain**) in the control in the right bottom corner but on the y axis is labeled **loss** which …
Comment: Use with_go along with other filters in getBM function by RuBBiT0 ▴ 10
Thank you! I think that makes much sense to me.
Comment: Interpret plot from DiffBind by Rory Stark ★ 4.9k
Not necessarily. It look to me like there is reconfiguring going on, with some chromatin that was open in the control becoming closed (the …
Comment: Interpret plot from DiffBind by Chris • 0
Thanks Rory! So that means the diseased sample has chromatin more open then the control one, is that correct?
Votes
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
Awards • All
Scholar to Mike Smith ★ 6.0k
Popular Question to Martin Morgan 25k
Teacher to deeenes ▴ 30
Popular Question to Hervé Pagès 16k
Popular Question to Gordon Smyth 47k
Locations • All
EMBL Heidelberg, 1 minute ago
United States, 12 minutes ago
United States, 15 minutes ago
United States, 16 minutes ago
Germany, 19 minutes ago
Traffic: 389 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6