Showing : Enrichment • reset
1
vote
4
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881
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GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment GSVA ssGSEA
updated 8 weeks ago by ▴ 10 • written 11 weeks ago by ▴ 10
0
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0
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627
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topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
20 months ago Priya • 0
0
votes
4
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1.7k
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Questions about non-model organisms gene enrichment analysis
non-model enrichment organisms analysis
updated 2.0 years ago by ★ 4.1k • written 2.2 years ago by • 0
0
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0
replies
662
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Enrichment in genomic regions
Enrichment clusterPro WGCNA
2.5 years ago María José • 0
0
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2
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1.2k
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Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression GeneExpression R enrichment DEGseq
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by • 0
1
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3
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2.5k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 10 months ago by • 0 • written 2.5 years ago by • 0
1
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3
replies
7.8k
views
GSVA and ssGSEA output differences
enrichment GSVA enrichplot ssGSEA
updated 2.7 years ago by ★ 3.4k • written 2.7 years ago by • 0
0
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0
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764
views
Over-enrichment of cytobands in INDUCE-Seq
enrichment INDUCE-Seq
3.2 years ago Mark Dunning ★ 1.1k
2
votes
2
replies
1.1k
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Hypergeometric (gene set enrichment) test using "Categories" package
enrichment hypergeometric Categories
3.6 years ago josmantorres ▴ 10
0
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7
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3.2k
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topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 4.1 years ago by 52k • written 4.1 years ago by ▴ 20
4
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4
replies
1.6k
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 4.3 years ago by 52k • written 4.3 years ago by ▴ 120
1
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2
replies
11k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by • 0
0
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0
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938
views
reactomePA error input file
r reactomePA enrichment
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by ▴ 10
3
votes
3
replies
6.1k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 18 months ago by ★ 4.1k • written 4.7 years ago by • 0
5
votes
7
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2.7k
views
Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 4.7 years ago by 52k • written 4.7 years ago by ▴ 60
2
votes
1
reply
1.7k
views
Multiple protein ids issue- which protein IDs should be selected for downstream analysis?
Proteomics enrichment Perseus
4.8 years ago harelarik ▴ 60
3
votes
3
replies
1.5k
views
Discrepancies between topGO output and input
go topGO gene ontology enrichment
updated 5.5 years ago by 67k • written 5.5 years ago by • 0
1
vote
1
reply
1.3k
views
How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
5.9 years ago David ROUX ▴ 20
2
votes
3
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1.2k
views
How to calculate overlap between transposable elements differentially expressed in one experiment, with those expressed in another set of samples?
gene expression enrichment RNA-seq DESeq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 40
0
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0
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1.0k
views
how to: enrichment (over representation) analysis of GWAS/QTL data distributed over a genome with GOSEQ
goseq enrichment GWAS
6.3 years ago zhu • 0
0
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0
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1.3k
views
Enrichment of GWAS SNPs in regulatory regions
genomicranges enrichment fisher
8.2 years ago enricoferrero ▴ 660
1
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2
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2.5k
views
Bias correction for enrichment analysis of 450k methylation data => feed bias adjusted genes into IPA
goseq 450k enrichment
updated 9.8 years ago by ▴ 40 • written 9.8 years ago by ▴ 10
0
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0
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1.9k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
10.1 years ago Guangchuang Yu ★ 1.2k
23 results • Page 1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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