Showing : DOSE • reset
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compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 17 days ago by ★ 3.9k • written 21 days ago by • 0
1
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2
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5.5k
views
ClusterProfiler DotPlot Vs Ridgeplot
clusterProfiler DOSE
updated 16 months ago by • 0 • written 20 months ago by • 0
4
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4
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4.2k
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Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 18 months ago by • 0 • written 7.7 years ago by ▴ 660
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3
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3.6k
views
Unable to generate a dotplot to view the enrichment analysis results (clusterProfiler/ enrichplot)
clusterProfiler enrichplot clusterpro doseR dose
updated 21 months ago by ★ 3.9k • written 22 months ago by ▴ 10
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0
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843
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enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.2 years ago Lluís Revilla Sancho ▴ 730
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0
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757
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Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
3.4 years ago Madza Farias-Virgens • 0
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2
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2.0k
views
DO.db is missing after repeated installations-ReactomePA-ClusterProfiler-DOSE
software error reactomePA DOSE DO.db there is no package called ‘DO.db’
updated 4.4 years ago by 25k • written 4.4 years ago by • 0
0
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1
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731
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Disease semantic similarity
DOSE
5.0 years ago ahmettoprak42 • 0
0
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1
reply
989
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How to change the siez of lables in heatmap
software error go dose heatplot gseGo
5.3 years ago aboumarshal • 0
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0
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1.5k
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Moving around nodes using emapplot {enrichplot} or enrichMap {DOSE}
enrichment map emapplot enrichplot enrichMap DOSE
5.9 years ago jan.soderman • 0
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1
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1.2k
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dotplot in DOSE
compilation error DOSE
6.0 years ago alper.kucukural ▴ 10
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2
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1.6k
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Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 6.3 years ago by ★ 1.2k • written 6.3 years ago by • 0
2
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2
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3.5k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by ▴ 10
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4
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3.1k
views
gseDO function input
DOSE clusterprofiler
updated 6.7 years ago by ★ 1.2k • written 6.7 years ago by • 0
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3
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1.2k
views
Failed to install 'DOSE' package. Win10, 'single candle'
DOSE package installation windows10
6.8 years ago Yisong Zhen ▴ 200
1
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3
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1.6k
views
Subset of genes can find a term but whole set cannot
biomart dose
updated 6.9 years ago by 65k • written 6.9 years ago by • 0
2
votes
5
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1.8k
views
Need help setting up DESeq2 complex model for multi-dose experiment
deseq2 multiple time points dose
updated 7.2 years ago by 41k • written 7.2 years ago by • 0
1
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1
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1.6k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
7.3 years ago Kajus Baidžajevas ▴ 10
4
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3
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1.8k
views
BiocParallel: object export issue
BiocParallel DOSE
updated 7.5 years ago by 25k • written 7.5 years ago by ★ 3.9k
2
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6
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3.1k
views
leading edge analysis clusterProfiler DOSE custom GSEA
clusterprofiler DOSE GSEA_internal USER_DATA leading edge Analysis
7.6 years ago Riba Michela ▴ 90
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0
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2.7k
views
Modifying the legend in cnetplot function
clusterProfiler DOSE
8.4 years ago Vinicius Henrique da Silva ▴ 40
1
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1
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1.6k
views
Treatment dose in treatment-control RNA-seq
deseq2 edger dose rna-seq
updated 8.5 years ago by ★ 28k • written 8.5 years ago by • 0
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0
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1.7k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
9.5 years ago Guangchuang Yu ★ 1.2k
0
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1
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1.4k
views
strange log2FoldChange estimates
RNASeq DOSE DESeq2 RNASeq DOSE DESeq2
9.7 years ago Shi, Tao ▴ 720
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2
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1.8k
views
question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray DOSE Microarray DOSE
updated 10.4 years ago by ▴ 190 • written 10.4 years ago by ★ 13k
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0
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1.7k
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question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray limma DOSE Microarray limma DOSE
10.4 years ago Gordon Smyth 50k
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0
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1.4k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO Cancer Rgraphviz clusterProfiler DOSE GO Cancer Rgraphviz clusterProfiler DOSE
10.8 years ago Martin Morgan 25k
0
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3
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1.8k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO clusterProfiler DOSE GO clusterProfiler DOSE
updated 10.8 years ago by ★ 8.2k • written 10.8 years ago by ★ 13k
0
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0
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1.1k
views
Identifying expression trends in RNA-seq experiment - through edgeR
edgeR DOSE edgeR DOSE
10.8 years ago Sandhya Pemmasani Kiran ▴ 40
0
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1
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2.1k
views
Question on unbalanced paired design
Microarray Normalization GO limma DOSE Microarray Normalization GO limma DOSE
updated 11.1 years ago by ★ 7.9k • written 11.1 years ago by ▴ 40
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2
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1.3k
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about limma linear models
Microarray limma DOSE Microarray limma DOSE
updated 13.0 years ago by ▴ 40 • written 13.0 years ago by 50k
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1
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1.5k
views
LIMMA: donor effect
Microarray limma DOSE Microarray limma DOSE
updated 13.0 years ago by ▴ 380 • written 13.0 years ago by 50k
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0
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1.5k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
13.4 years ago Roman ▴ 20
0
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2
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1.5k
views
FW: PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
updated 13.4 years ago by ▴ 120 • written 13.4 years ago by ▴ 10
0
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2
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1.8k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
updated 13.4 years ago by ★ 4.3k • written 13.4 years ago by ▴ 120
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2
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2.5k
views
Regression using LIMMA
affy limma DOSE affy limma DOSE
updated 13.5 years ago by ★ 6.0k • written 13.5 years ago by ▴ 380
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1
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1.2k
views
limma: writing down the matrix in an almost (?) factorial design experiment
Microarray DOSE Microarray DOSE
14.2 years ago Massimo Pinto ▴ 390
0
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9
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4.5k
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GEOquery installation problem
DOSE DOSE
14.8 years ago zhihua zhang ▴ 50
0
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4
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1.6k
views
GEO annotation
Annotation DOSE Annotation DOSE
updated 15.9 years ago by ★ 7.2k • written 15.9 years ago by ▴ 110
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5
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3.0k
views
Finding genes with significant linear regression or trend
Microarray Regression Cancer limma DOSE Microarray Regression Cancer limma DOSE
updated 16.0 years ago by ▴ 340 • written 16.0 years ago by ★ 1.9k
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0
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1.2k
views
Expired Illumina expression chip - advice for use and experimental design
GO limma DOSE GO limma DOSE
16.3 years ago Johnstone, Alice ▴ 410
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0
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1.1k
views
about microarray batch effect and treatment effect
affy DOSE affy DOSE
16.4 years ago Aedin Culhane ▴ 510
0
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0
replies
1.2k
views
microarray analysis of a dose response * strain experiment
Microarray affy limma maSigPro DOSE BRAIN Microarray affy limma maSigPro DOSE BRAIN
17.5 years ago Naomi Altman ★ 6.0k
0
votes
4
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1.5k
views
microarray analysis of a dose response * strain experiment
affy DOSE BRAIN affy DOSE BRAIN
updated 17.5 years ago by 21k • written 17.5 years ago by ▴ 890
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1
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1.5k
views
Re: Limma: M value in toptable
limma DOSE limma DOSE
updated 19.2 years ago by ▴ 60 • written 19.2 years ago by 50k
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0
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1.6k
views
RMA normalization,which samples should be normalized together
Normalization probe affy limma gcrma DOSE Normalization probe affy limma gcrma DOSE
19.2 years ago Dipl.-Ing. Johannes Rainer ▴ 430
0
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1
reply
2.1k
views
Dose-Response: Regressiion and ANOVA
Regression DOSE Regression DOSE
updated 19.3 years ago by ▴ 360 • written 19.3 years ago by ▴ 620
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1
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1.2k
views
normalizaton between studies
Normalization vsn DOSE Normalization vsn DOSE
updated 19.4 years ago by ▴ 10 • written 19.4 years ago by ▴ 620
0
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1
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1.3k
views
unbalanced design
limma DOSE limma DOSE
updated 19.4 years ago by 50k • written 19.4 years ago by ▴ 620
0
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0
replies
1.1k
views
Friedman test
DOSE DOSE
19.7 years ago Arne.Muller@aventis.com ▴ 620
50 results • Page 1 of 1
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Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
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A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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