Showing : goseq • reset
5
votes
9
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2.0k
views
Inconsistent nullp and goseq enrichment results across operating systems
goseq
written 5 months ago by • 0
2
votes
3
replies
874
views
package goseq seems to be not available on the latest version of R
goseq
updated 7 months ago by 52k • written 7 months ago by ▴ 20
1
vote
2
replies
530
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq Bioconductor rtracklayer
9 months ago thomas • 0
1
vote
4
replies
794
views
goseq, warning and strange plot from nullp
goseq
10 months ago boczniak767 ▴ 740
0
votes
1
reply
796
views
Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 2.1 years ago by ▴ 10 • written 2.1 years ago by • 0
0
votes
5
replies
2.7k
views
GO enrichment with non-model organism, supplying GO mappings
clusterProfiler goseq topGO DESeq2
updated 2.6 years ago by 67k • written 2.6 years ago by ▴ 30
0
votes
2
replies
1.1k
views
goseq: Wallenius Vs Fisher's Noncentral Hypergeometric Distribution
goseq
2.6 years ago Steve Pederson ▴ 170
1
vote
2
replies
1.1k
views
Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
2.8 years ago • updated 2.7 years ago m.glymenaki • 0
0
votes
0
replies
951
views
Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
1
vote
10
replies
3.0k
views
How to run Goseq for list of ensembl gene IDs
goseq
3.7 years ago Lucky • 0
1
vote
4
replies
1.8k
views
goseq package loading issues
DESeq2 goseq
3.8 years ago avinashi • 0
3
votes
9
replies
2.3k
views
Warning message when performing Gene Ontology analysis with goseq using hg38
goseq
updated 3.8 years ago by 67k • written 3.8 years ago by • 0
2
votes
3
replies
2.1k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 3.9 years ago by 67k • written 3.9 years ago by ▴ 30
2
votes
2
replies
1.4k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.0 years ago by 67k • written 4.0 years ago by • 0
0
votes
1
reply
1.1k
views
non-native GO annotation cannot be successfully introduced into Goseq
goseq rnaseq r
updated 4.2 years ago by 67k • written 4.2 years ago by • 0
1
vote
2
replies
1.1k
views
GOSeq analysis in rice
goseq
4.5 years ago • updated 4.3 years ago Jitendra ▴ 10
0
votes
2
replies
865
views
Goseq_analysis related help
goseq
4.5 years ago kumararya563 • 0
0
votes
0
replies
598
views
go seq related help, where I need to do mapping between go term and the protein -id
goseq
4.5 years ago kumararya563 • 0
3
votes
2
replies
1.3k
views
Goseq analysis related help.
annotation goseq
updated 4.5 years ago by ★ 13k • written 4.5 years ago by • 0
0
votes
0
replies
1.0k
views
How to identify differentially expressed genes from Reactome pathways enriched according to GOseq?
goseq go rna-seq
4.7 years ago hasse.bossenbroek • 0
4
votes
5
replies
2.1k
views
Downgrading R to 3.6.0 version (GOseq problem)
goseq installation
5.0 years ago gdalsky ▴ 40
0
votes
1
reply
2.5k
views
GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment gene ontology goseq go
5.2 years ago Raito92 ▴ 60
2
votes
6
replies
1.4k
views
Can't install GOSEQ (dependency problem) on CentOS 7!
goseq r package r
updated 5.3 years ago by ★ 6.6k • written 5.3 years ago by ▴ 60
2
votes
1
reply
1.8k
views
GOseq analysis with only upregulated or downregulated genes
goseq
updated 5.7 years ago by ▴ 320 • written 5.7 years ago by ▴ 160
2
votes
2
replies
1.3k
views
Using GOseq for custom gene set enrichment test
goseq
updated 5.9 years ago by 52k • written 5.9 years ago by • 0
2
votes
2
replies
3.5k
views
How to access gene IDs associated with GO terms in GOSeq
GOseq ensemblid GO
updated 6.1 years ago by 67k • written 6.1 years ago by • 0
4
votes
10
replies
3.4k
views
Question: GoSeq: opposite pwf plot for up- and downregulated genes
goseq
9.2 years ago • updated 6.1 years ago Jakub ▴ 50
1
vote
3
replies
2.1k
views
goseq: Formatting category list for use with goseq
goseq category test
updated 6.2 years ago by 67k • written 6.2 years ago by ▴ 40
0
votes
0
replies
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
votes
1
reply
1.3k
views
GOseq output but strange warning message!
GOseq GO pwf goseq
6.3 years ago TB18 • 0
1
vote
1
reply
1.4k
views
Goseq output with too many GO terms per category
go goseq goterm category
updated 6.4 years ago by 52k • written 6.4 years ago by • 0
3
votes
2
replies
1.2k
views
numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
goseq
updated 6.4 years ago by 67k • written 6.4 years ago by • 0
1
vote
9
replies
2.5k
views
Using goseq with unsupported organism
goseq
updated 6.4 years ago by 67k • written 6.4 years ago by • 0
0
votes
0
replies
1.1k
views
GOseq No Underrepresented Categories
goseq go enrichment
6.5 years ago mart1139 • 0
8
votes
10
replies
1.9k
views
Genes listed in GO categories
goseq biomart
updated 6.5 years ago by 52k • written 6.5 years ago by • 0
0
votes
2
replies
1.0k
views
goseq with hypergeometric method
goseq
updated 6.5 years ago by 52k • written 6.5 years ago by ▴ 40
0
votes
0
replies
1.5k
views
I finally solved my problem with installing "org.Hs.eg.db"!
goseq org.hs.eg.db
6.7 years ago nancyjwahl7 • 0
2
votes
6
replies
2.3k
views
Can Tximport average transcript length be used for GOSeq?
deseq2 tximport goseq
6.8 years ago casey.rimland ▴ 170
0
votes
6
replies
1.7k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq methylation ensembl ucsc limma
6.8 years ago dusan.petrovic • 0
0
votes
2
replies
4.0k
views
DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2 goseq rnaseq go enrichment differential gene expression
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
0
votes
3
replies
1.5k
views
What is the impact of using GOSeq to voom-adjusted RNA-seq Expressions ?
limma limma-voom goseq
updated 6.9 years ago by 52k • written 6.9 years ago by • 0
0
votes
1
reply
2.8k
views
installation of package 'goseq' had non-zero exit status
goseq installation
updated 7.0 years ago by 25k • written 7.0 years ago by • 0
0
votes
1
reply
1.9k
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 7.0 years ago by 67k • written 7.0 years ago by ▴ 10
1
vote
2
replies
3.2k
views
GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
goseq gene ontology
updated 7.2 years ago by 67k • written 7.2 years ago by • 0
0
votes
1
reply
1.3k
views
Error: subscript out of bounds when using ucscGenomes() and supportedGenomes() functions in goseq and rtracklayer packages respctively
goseq rtracklayer
7.2 years ago mgdrnl • 0
2
votes
3
replies
2.0k
views
GOseq error on running nullp
goseq GO term
updated 7.2 years ago by 52k • written 7.2 years ago by • 0
0
votes
1
reply
2.1k
views
GO.db won't install for using goseq package
GO.db goseq package installation error
updated 7.3 years ago by 25k • written 7.3 years ago by • 0
0
votes
2
replies
1.8k
views
bias.data vector must have the same length as DEgenes vector!
edger goseq
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 10
0
votes
0
replies
1.5k
views
gene length file for GOseq
goseq
7.3 years ago mictadlo ▴ 10
2
votes
2
replies
1.7k
views
Error in normSplitFactor(f, x)
GenomicRanges rtracklayer goseq
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ▴ 10
50 results • Page 1 of 1
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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!
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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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