Showing : dose • reset
2
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3
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Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
11 months ago Yifeii.Ge • 0
1
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4
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1.4k
views
Error in gseDO function
DOSE gsea
17 months ago • updated 16 months ago Javier • 0
0
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2
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2.6k
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compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 8 weeks ago by • 0 • written 18 months ago by • 0
4
votes
4
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6.0k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 3.0 years ago by • 0 • written 9.1 years ago by ▴ 680
1
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2
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11k
views
ClusterProfiler DotPlot Vs Ridgeplot
clusterProfiler DOSE
updated 2.8 years ago by • 0 • written 3.1 years ago by • 0
0
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3
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6.4k
views
Unable to generate a dotplot to view the enrichment analysis results (clusterProfiler/ enrichplot)
clusterProfiler enrichplot clusterpro doseR dose
updated 3.3 years ago by ★ 4.1k • written 3.3 years ago by ▴ 10
0
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0
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1.2k
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
4.7 years ago Lluís Revilla Sancho ▴ 760
0
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0
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1.1k
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Functional enrichment analysis for genomic data from non-model organism annotated based on model organism
DOSE hypeR goTools GOstats topGO
4.9 years ago Madza Farias-Virgens • 0
0
votes
2
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2.8k
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 5.9 years ago by 25k • written 5.9 years ago by • 0
0
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1
reply
1.1k
views
Disease semantic similarity
DOSE
6.5 years ago ahmettoprak42 • 0
0
votes
1
reply
1.3k
views
How to change the siez of lables in heatmap
software error go dose heatplot gseGo
6.7 years ago aboumarshal • 0
0
votes
0
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2.1k
views
Moving around nodes using emapplot {enrichplot} or enrichMap {DOSE}
enrichment map emapplot enrichplot enrichMap DOSE
7.4 years ago jan.soderman • 0
1
vote
1
reply
1.7k
views
dotplot in DOSE
compilation error DOSE
7.5 years ago alper.kucukural ▴ 10
0
votes
2
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2.1k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 7.7 years ago by ★ 1.2k • written 7.7 years ago by • 0
2
votes
2
replies
4.6k
views
enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 7.9 years ago by ★ 1.2k • written 7.9 years ago by ▴ 20
1
vote
4
replies
4.2k
views
gseDO function input
DOSE clusterprofiler
updated 8.2 years ago by ★ 1.2k • written 8.2 years ago by • 0
0
votes
3
replies
1.9k
views
Failed to install 'DOSE' package. Win10, 'single candle'
DOSE package installation windows10
8.3 years ago Yisong Zhen ▴ 200
1
vote
3
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2.1k
views
Subset of genes can find a term but whole set cannot
biomart dose
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
2
votes
5
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2.3k
views
Need help setting up DESeq2 complex model for multi-dose experiment
deseq2 multiple time points dose
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
1
vote
1
reply
2.0k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
8.8 years ago Kajus Baidžajevas ▴ 10
4
votes
3
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2.8k
views
BiocParallel: object export issue
BiocParallel DOSE
updated 9.0 years ago by 25k • written 9.0 years ago by ★ 4.1k
2
votes
6
replies
4.4k
views
leading edge analysis clusterProfiler DOSE custom GSEA
clusterprofiler DOSE GSEA_internal USER_DATA leading edge Analysis
9.1 years ago • updated 9.0 years ago Riba Michela ▴ 90
0
votes
0
replies
3.4k
views
Modifying the legend in cnetplot function
clusterProfiler DOSE
9.9 years ago Vinicius Henrique da Silva ▴ 40
1
vote
1
reply
2.0k
views
Treatment dose in treatment-control RNA-seq
deseq2 edger dose rna-seq
updated 10.0 years ago by ★ 29k • written 10.0 years ago by • 0
0
votes
0
replies
2.1k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
10.9 years ago Guangchuang Yu ★ 1.2k
0
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1
reply
1.7k
views
strange log2FoldChange estimates
RNASeq DOSE DESeq2 RNASeq DOSE DESeq2
11.2 years ago Shi, Tao ▴ 720
0
votes
2
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2.2k
views
question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray DOSE Microarray DOSE
updated 11.9 years ago by ▴ 190 • written 11.9 years ago by ★ 13k
0
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0
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2.0k
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question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray limma DOSE Microarray limma DOSE
11.9 years ago Gordon Smyth 53k
0
votes
0
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1.7k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO Cancer Rgraphviz clusterProfiler DOSE GO Cancer Rgraphviz clusterProfiler DOSE
12.3 years ago Martin Morgan 25k
0
votes
3
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2.4k
views
Error in clusterProfiler package with function \"setReadable<-\"
GO clusterProfiler DOSE GO clusterProfiler DOSE
updated 12.3 years ago by ★ 8.2k • written 12.3 years ago by ★ 13k
0
votes
0
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1.4k
views
Identifying expression trends in RNA-seq experiment - through edgeR
edgeR DOSE edgeR DOSE
12.3 years ago Sandhya Pemmasani Kiran ▴ 40
0
votes
1
reply
2.4k
views
Question on unbalanced paired design
Microarray Normalization GO limma DOSE Microarray Normalization GO limma DOSE
updated 12.5 years ago by ★ 7.9k • written 12.5 years ago by ▴ 40
0
votes
2
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1.7k
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about limma linear models
Microarray limma DOSE Microarray limma DOSE
updated 14.4 years ago by ▴ 40 • written 14.4 years ago by 53k
0
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1
reply
2.0k
views
LIMMA: donor effect
Microarray limma DOSE Microarray limma DOSE
updated 14.5 years ago by ▴ 380 • written 14.5 years ago by 53k
0
votes
0
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1.8k
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PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
14.8 years ago Roman ▴ 20
0
votes
2
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2.0k
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 14.9 years ago by ▴ 120 • written 14.9 years ago by ▴ 10
0
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2
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2.1k
views
PLANdbAffy + Alternative Exon Annotation +XPS, aroma, oligo, RMAExpress
Annotation cdf probe affy oligo xps DOSE Annotation cdf probe affy oligo xps DOSE
updated 14.9 years ago by ★ 4.3k • written 14.9 years ago by ▴ 120
1
vote
2
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2.8k
views
Regression using LIMMA
affy limma DOSE affy limma DOSE
updated 15.0 years ago by ★ 6.0k • written 15.0 years ago by ▴ 380
0
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1
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1.6k
views
limma: writing down the matrix in an almost (?) factorial design experiment
Microarray DOSE Microarray DOSE
15.7 years ago Massimo Pinto ▴ 390
0
votes
9
replies
5.7k
views
GEOquery installation problem
DOSE DOSE
16.2 years ago zhihua zhang ▴ 50
0
votes
4
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2.0k
views
GEO annotation
Annotation DOSE Annotation DOSE
updated 17.4 years ago by ★ 7.2k • written 17.4 years ago by ▴ 110
0
votes
5
replies
3.6k
views
Finding genes with significant linear regression or trend
Microarray Regression Cancer limma DOSE Microarray Regression Cancer limma DOSE
updated 17.4 years ago by ▴ 340 • written 17.4 years ago by ★ 1.9k
0
votes
0
replies
1.5k
views
Expired Illumina expression chip - advice for use and experimental design
GO limma DOSE GO limma DOSE
17.7 years ago Johnstone, Alice ▴ 410
0
votes
0
replies
1.4k
views
about microarray batch effect and treatment effect
affy DOSE affy DOSE
17.8 years ago Aedin Culhane ▴ 510
0
votes
0
replies
1.4k
views
microarray analysis of a dose response * strain experiment
Microarray affy limma maSigPro DOSE BRAIN Microarray affy limma maSigPro DOSE BRAIN
19.0 years ago Naomi Altman ★ 6.0k
0
votes
4
replies
2.0k
views
microarray analysis of a dose response * strain experiment
affy DOSE BRAIN affy DOSE BRAIN
updated 19.0 years ago by 21k • written 19.0 years ago by ▴ 890
0
votes
1
reply
1.8k
views
Re: Limma: M value in toptable
limma DOSE limma DOSE
updated 20.7 years ago by ▴ 60 • written 20.7 years ago by 53k
0
votes
0
replies
2.1k
views
RMA normalization,which samples should be normalized together
Normalization probe affy limma gcrma DOSE Normalization probe affy limma gcrma DOSE
20.7 years ago Dipl.-Ing. Johannes Rainer ▴ 430
0
votes
1
reply
2.5k
views
Dose-Response: Regressiion and ANOVA
Regression DOSE Regression DOSE
updated 20.8 years ago by ▴ 360 • written 20.8 years ago by ▴ 620
0
votes
1
reply
1.5k
views
normalizaton between studies
Normalization vsn DOSE Normalization vsn DOSE
updated 20.9 years ago by ▴ 10 • written 20.9 years ago by ▴ 620
67 results • Page 1 of 2
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Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Was anyone else able to put the pieces together using the reply above? I read in one 10X sample using DropletUtils::read10xCounts() and thi…
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by dzv20413 • 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments by Erik Wright ▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Comment: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by Gabriel • 0
Thank you very much for the reply. However, none of these three options seems to fit: 1) The genes for which NA appears do not have all 0 …
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by ubjw24 • 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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