Showing : go • reset
0
votes
0
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1.0k
views
Differential Expressed Genes analysis regarding limited genes
Sequencing Normalization GO DESeq Sequencing Normalization GO DESeq
12.2 years ago Michael Love 43k
0
votes
1
reply
1.4k
views
topGO analysis returns different gene counts for category than given for non-model organism
Annotation GO topGO Annotation GO topGO
updated 12.2 years ago by ▴ 20 • written 12.2 years ago by ▴ 400
0
votes
0
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2.2k
views
sva + voom + limma. eBayes(trend=TRUE)
GO GO
12.2 years ago Meritxell Oliva ▴ 120
0
votes
1
reply
1.8k
views
topGO analysis returns different gene counts for category than given for non-model organism
GO Category topGO GO Category topGO
updated 12.2 years ago by ★ 6.8k • written 12.2 years ago by ▴ 20
0
votes
0
replies
766
views
Error while background correction
GO probe GO probe
12.2 years ago kunal jha ▴ 10
0
votes
0
replies
1.0k
views
question on ChIPpeakAnno::getEnrichedGO
GO ChIPpeakAnno GO ChIPpeakAnno
12.2 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
2.5k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
12.2 years ago Sarah Pohl ▴ 30
0
votes
2
replies
2.1k
views
BiomaRt useMart() issues
GO GO
updated 12.2 years ago by ▴ 540 • written 12.2 years ago by ▴ 200
0
votes
1
reply
865
views
DESeq query
GO DESeq GO DESeq
updated 12.2 years ago by 43k • written 12.2 years ago by ▴ 40
0
votes
0
replies
1.6k
views
error while using goProfiles package on arabidopsis entrez gene IDs
GO Organism goProfiles GO Organism goProfiles
12.2 years ago Marc Carlson ★ 7.2k
0
votes
2
replies
2.5k
views
problem with makeOrgPackageFromNCBI (for Chinese hamster)
Annotation GO db0 PROcess Annotation GO db0 PROcess
updated 12.2 years ago by ★ 7.2k • written 12.2 years ago by ★ 4.1k
0
votes
0
replies
1.7k
views
error of \"subscript out of bounds\" while applying basicProfile func
GO GO
12.2 years ago Marc Carlson ★ 7.2k
0
votes
3
replies
1.5k
views
defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package
Annotation GO Organism AnnotationDbi Annotation GO Organism AnnotationDbi
12.2 years ago Sashi ▴ 20
0
votes
0
replies
1.2k
views
question about package AgiMicroRna
Normalization GO vsn Normalization GO vsn
12.2 years ago Guest User ★ 13k
0
votes
3
replies
4.1k
views
saving GRanges objects - resulting file size issue
GO GO
updated 12.2 years ago by ★ 6.8k • written 12.2 years ago by ▴ 120
0
votes
5
replies
2.7k
views
problem generating Chinese hamster txdb from GFF file
GO GenomicFeatures GO GenomicFeatures
updated 3 months ago by • 0 • written 12.2 years ago by ★ 4.1k
0
votes
3
replies
2.4k
views
Diffbind: Binding Affinity Heatmap
Sequencing GO Clustering GLAD edgeR DESeq DiffBind Sequencing GO Clustering GLAD edgeR
12.2 years ago Rory Stark ★ 5.2k
0
votes
0
replies
2.5k
views
topgo GO mapping for non model organisms
Annotation GO Organism topGO Annotation GO Organism topGO
12.2 years ago km ▴ 100
1
vote
4
replies
5.0k
views
[topGO] More flexible way to select 'interesting' genes
GO probe topGO GO probe topGO
updated 12.3 years ago by ▴ 400 • written 12.3 years ago by ▴ 680
0
votes
0
replies
1.4k
views
bioMart GO inconsistency, normal?
GO biomaRt GO biomaRt
12.3 years ago R Tagett ▴ 30
0
votes
0
replies
793
views
R package cleanUpdTSeq
GO GO
12.3 years ago Ou, Jianhong ★ 1.3k
0
votes
1
reply
1.4k
views
Error in .testGOFrame(x, organism) and invalid GO Evidence codes
GO Organism GO Organism
updated 12.3 years ago by ★ 7.2k • written 12.3 years ago by ▴ 10
0
votes
5
replies
2.2k
views
Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis
Annotation GO BSgenome cdf BSgenome Rsubread Annotation GO BSgenome cdf BSgenome
12.3 years ago Alan Smith ▴ 150
0
votes
0
replies
1.4k
views
Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis
Annotation GO BSgenome cdf BSgenome Rsubread Annotation GO BSgenome cdf BSgenome
12.3 years ago Wei Shi ★ 3.6k
0
votes
0
replies
1.5k
views
Rsubread - featureCounts for extracting read counts from De novo assembled transcripts
Annotation GO BSgenome cdf BSgenome Rsubread Annotation GO BSgenome cdf BSgenome
12.3 years ago Wei Shi ★ 3.6k
0
votes
0
replies
1.6k
views
RIPSeeker multicore option not working fully?
GO biomaRt RIPSeeker GO biomaRt RIPSeeker
12.3 years ago Davis, Wade ▴ 350
0
votes
0
replies
1.3k
views
Rsubread - featureCounts for extracting read counts from De novo assembled transcripts
Annotation GO BSgenome BSgenome Annotation GO BSgenome BSgenome
12.3 years ago Alan Smith ▴ 150
0
votes
0
replies
3.1k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
12.3 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
1.5k
views
RIPSeeker multicore option not working fully?
Annotation GO RIPSeeker Annotation GO RIPSeeker
updated 12.3 years ago by ★ 8.2k • written 12.3 years ago by ▴ 350
0
votes
1
reply
761
views
Error in extracting genes from Goterms using GOStats package
Annotation GO GOstats Annotation GO GOstats
updated 12.3 years ago by 68k • written 12.3 years ago by ★ 13k
0
votes
1
reply
1.3k
views
convert IDs in a data frame?
GO Infrastructure Cancer GO Infrastructure Cancer
updated 12.3 years ago by ★ 7.2k • written 12.3 years ago by 16k
0
votes
2
replies
929
views
Problem with decideTests - No p-val correction
GO GO
updated 12.3 years ago by 68k • written 12.3 years ago by ▴ 310
0
votes
1
reply
630
views
Prolems with AraGene 1_1 annotation
Annotation GO cdf probe Annotation GO cdf probe
updated 12.3 years ago by 68k • written 12.3 years ago by ▴ 10
0
votes
3
replies
1.9k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
12.3 years ago Alan Smith ▴ 150
0
votes
2
replies
1.5k
views
limma for homemade microarray - question on NAs and multiple probes for one gene
Microarray Normalization GO Network Cancer probe limma Microarray Normalization GO probe
updated 12.3 years ago by 53k • written 12.3 years ago by ★ 3.0k
0
votes
0
replies
1.9k
views
Correcting for batch effect between two batches of interleaved timepoints
Normalization GO limma edgeR Normalization GO limma edgeR
12.3 years ago Ryan C. Thompson ★ 7.9k
0
votes
3
replies
1.5k
views
simple
GO simpleaffy GO simpleaffy
updated 12.3 years ago by 68k • written 12.3 years ago by ★ 13k
0
votes
0
replies
1.8k
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
1
reply
2.0k
views
nsFilter error in genefilter
GO hgu133plus2 cdf GSVA AnnotationForge GO hgu133plus2 cdf GSVA AnnotationForge
updated 12.3 years ago by 68k • written 12.4 years ago by ▴ 90
0
votes
3
replies
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
replies
1.2k
views
Problem running pathview due to broken XML package
GO pathview GO pathview
12.4 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
1.1k
views
using a gtf file to map reads
GO GenomicFeatures DEXSeq GO GenomicFeatures DEXSeq
updated 12.4 years ago by ★ 1.9k • written 12.4 years ago by ★ 6.8k
0
votes
2
replies
1.7k
views
lumiR returns ExpressionSet object instead of LumiBatch
GO Mus musculus BSgenome BSgenome lumi GO Mus musculus BSgenome BSgenome lumi
updated 12.4 years ago by ▴ 440 • written 12.4 years ago by ★ 13k
0
votes
1
reply
1.3k
views
edgeR outlier question for version 3.0.8
RNASeq GO edgeR RNASeq GO edgeR
updated 12.4 years ago by 53k • written 12.4 years ago by ▴ 340
0
votes
2
replies
1.7k
views
Gviz error with collapseTranscripts=TRUE
GO Gviz GO Gviz
updated 12.4 years ago by ★ 1.6k • written 12.4 years ago by ▴ 890
0
votes
5
replies
1.9k
views
TXNAME mapping
GO BSgenome BSgenome GO BSgenome BSgenome
updated 12.4 years ago by ▴ 90 • written 12.4 years ago by ★ 13k
0
votes
1
reply
1.5k
views
Unexpected results of differential expression analysis
GO limma siggenes GO limma siggenes
updated 12.4 years ago by ★ 13k • written 12.4 years ago by ★ 13k
3
votes
4
replies
4.5k
views
How to retrieve all GO terms at level 5 as well as their annotated genes
GO GO
12.4 years ago Peter Davidsen ▴ 210
0
votes
0
replies
610
views
summarizeOverlaps: ambiguous method dispatch
GO GO
12.4 years ago Valerie Obenchain ★ 6.8k
0
votes
4
replies
2.1k
views
FeatureExpressionSet using list.files() in place of read.xysfiles()
Microarray Annotation GO Organism probe annotate limma convert pdInfoBuilder sva GO sva
updated 12.4 years ago by ★ 4.3k • written 12.4 years ago by ▴ 140
1,936 results • Page 8 of 39
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Comment: Save the Date: BioC2026 by eja.gsssssswwse.r.m • 0
Que notícia incrivel sobre o BioC2026 Para quem gosta de aproveitar o conteudo online, também e possvel Baixar [snaptube versão antiga][1] …
Comment: Ensembl 115 has been released! by eja.gsssssswwse.r.m • 0
Keeping up with Ensembls latest release ensures access to cutting-edge genomic information. For those balancing research and leisure, a mob…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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