Showing : goseq • reset
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goseq: Wallenius Vs Fisher's Noncentral Hypergeometric Distribution
goseq
26 days ago • updated 25 days ago Steve Pederson ▴ 170
1
vote
2
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156
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
10 weeks ago • updated 8 weeks ago m.glymenaki • 0
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0
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96
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Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 10 weeks ago by 37k • written 10 weeks ago by • 0
1
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10
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971
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How to run Goseq for list of ensembl gene IDs
goseq
14 months ago • updated 13 months ago Lucky • 0
1
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4
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506
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goseq package loading issues
DESeq2 goseq
15 months ago avinashi • 0
3
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9
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698
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Warning message when performing Gene Ontology analysis with goseq using hg38
goseq
updated 15 months ago by 59k • written 15 months ago by • 0
2
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3
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565
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Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 16 months ago by 59k • written 16 months ago by ▴ 10
2
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2
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411
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Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 17 months ago by 59k • written 17 months ago by • 0
0
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1
reply
361
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non-native GO annotation cannot be successfully introduced into Goseq
goseq rnaseq r
updated 19 months ago by 59k • written 19 months ago by • 0
1
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2
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332
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GOSeq analysis in rice
goseq
23 months ago • updated 21 months ago nabiyogesh ▴ 10
0
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2
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247
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Goseq_analysis related help
goseq
23 months ago • updated 22 months ago kumararya563 • 0
0
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0
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196
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go seq related help, where I need to do mapping between go term and the protein -id
goseq
23 months ago • updated 22 months ago kumararya563 • 0
2
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2
replies
360
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Goseq analysis related help.
annotation goseq
updated 23 months ago by 13k • written 23 months ago by • 0
0
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0
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245
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How to identify differentially expressed genes from Reactome pathways enriched according to GOseq?
goseq go rna-seq
2.1 years ago hasse.bossenbroek • 0
4
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5
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987
views
Downgrading R to 3.6.0 version (GOseq problem)
goseq installation
2.4 years ago gdalsky ▴ 40
0
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1
reply
926
views
GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment gene ontology goseq go
2.7 years ago Raito92 ▴ 60
2
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6
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471
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Can't install GOSEQ (dependency problem) on CentOS 7!
goseq r package r
updated 2.7 years ago by ★ 5.5k • written 2.7 years ago by ▴ 60
1
vote
1
reply
565
views
GOseq analysis with only upregulated or downregulated genes
goseq
updated 3.1 years ago by ▴ 310 • written 3.1 years ago by ▴ 110
2
votes
2
replies
506
views
Using GOseq for custom gene set enrichment test
goseq
updated 3.3 years ago by 45k • written 3.3 years ago by • 0
0
votes
2
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966
views
How to access gene IDs associated with GO terms in GOSeq
GOseq ensemblid GO
updated 3.5 years ago by 59k • written 3.5 years ago by • 0
4
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10
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2.1k
views
Question: GoSeq: opposite pwf plot for up- and downregulated genes
goseq
6.6 years ago • updated 3.5 years ago Jakub ▴ 50
1
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3
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1.0k
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goseq: Formatting category list for use with goseq
goseq category test
updated 3.7 years ago by 59k • written 3.7 years ago by ▴ 30
0
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0
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457
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how to: enrichment (over representation) analysis of GWAS/QTL data distributed over a genome with GOSEQ
goseq enrichment GWAS
3.8 years ago zhu • 0
0
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1
reply
647
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GOseq output but strange warning message!
GOseq GO pwf goseq
3.8 years ago TB18 • 0
1
vote
1
reply
543
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Goseq output with too many GO terms per category
go goseq goterm category
updated 3.8 years ago by 45k • written 3.8 years ago by • 0
3
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2
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544
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numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
goseq
updated 3.8 years ago by 59k • written 3.8 years ago by • 0
1
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9
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1.1k
views
Using goseq with unsupported organism
goseq
updated 3.8 years ago by 59k • written 3.9 years ago by • 0
0
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0
replies
476
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GOseq No Underrepresented Categories
goseq go enrichment
3.9 years ago mart1139 • 0
8
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10
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787
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Genes listed in GO categories
goseq biomart
updated 3.9 years ago by 45k • written 4.0 years ago by • 0
0
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2
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510
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goseq with hypergeometric method
goseq
updated 4.0 years ago by 45k • written 4.0 years ago by ▴ 30
0
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0
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838
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I finally solved my problem with installing "org.Hs.eg.db"!
goseq org.hs.eg.db
4.1 years ago nancyjwahl7 • 0
2
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6
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1.1k
views
Can Tximport average transcript length be used for GOSeq?
deseq2 tximport goseq
4.2 years ago casey.rimland ▴ 140
0
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6
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817
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How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq methylation ensembl ucsc limma
4.3 years ago • updated 4.2 years ago dusan.petrovic • 0
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2
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2.4k
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DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2 goseq rnaseq go enrichment differential gene expression
updated 4.3 years ago by 37k • written 4.3 years ago by • 0
0
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3
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661
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What is the impact of using GOSeq to voom-adjusted RNA-seq Expressions ?
limma limma-voom goseq
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
0
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1
reply
2.1k
views
installation of package 'goseq' had non-zero exit status
goseq installation
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
0
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1
reply
1.1k
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 4.5 years ago by 59k • written 4.5 years ago by ▴ 10
1
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2
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2.1k
views
GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
goseq gene ontology
updated 4.6 years ago by 59k • written 4.6 years ago by • 0
0
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1
reply
748
views
Error: subscript out of bounds when using ucscGenomes() and supportedGenomes() functions in goseq and rtracklayer packages respctively
goseq rtracklayer
4.6 years ago mgdrnl • 0
2
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3
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923
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GOseq error on running nullp
goseq GO term
updated 4.6 years ago by 45k • written 4.6 years ago by • 0
0
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1
reply
1.5k
views
GO.db won't install for using goseq package
GO.db goseq package installation error
updated 4.7 years ago by 25k • written 4.7 years ago by • 0
0
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2
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980
views
bias.data vector must have the same length as DEgenes vector!
edger goseq
updated 4.7 years ago by ★ 27k • written 4.7 years ago by • 0
0
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0
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687
views
gene length file for GOseq
goseq
4.7 years ago mictadlo • 0
2
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2
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841
views
Error in normSplitFactor(f, x)
GenomicRanges rtracklayer goseq
updated 4.7 years ago by 11k • written 4.7 years ago by • 0
0
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3
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923
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goseq after edgeR
edger goseq
updated 4.7 years ago by ★ 27k • written 4.7 years ago by • 0
0
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2
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1.1k
views
GOseq: Correct for gene length or read count?
goseq dexseq
4.8 years ago • updated 4.7 years ago i.sudbery ▴ 30
1
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1
reply
2.0k
views
goseq: In pcls(G) : initial point very close to some inequality constraints
goseq warning message pwf mgcv
updated 4.7 years ago by ▴ 310 • written 4.8 years ago by ▴ 10
1
vote
1
reply
850
views
PANTHER.db function not found
pantherdb goseq biomart
updated 4.8 years ago by ★ 5.5k • written 4.8 years ago by ▴ 10
3
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5
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1.0k
views
Does DEseq2 analysis make GOseq redundant?
deseq2 goseq gene ontology differential gene expression
4.8 years ago david.rinker ▴ 10
0
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3
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1.6k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq gene ontology biomart annotate category
updated 4.9 years ago by ▴ 360 • written 4.9 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: CPM after RUVseq by James W. MacDonald 59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq by James W. MacDonald 59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq by Jess • 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error by Laurent Gatto 1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue by shepherl 3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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