Showing : organism • reset
0
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2
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1.1k
views
pdInfoBuilder fails on Affy's GeneChip Human Transcriptome Array 2.0
BiocViews Annotation Organism biocViews oligo oligoClasses BiocViews BiocViews Annotation
updated 5.9 years ago by ▴ 20 • written 7.2 years ago by ▴ 40
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962
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Re: KEGGprofile: "Error in phyper - Non-numeric argument to mathematical function" when using non model organism
Organism KEGGprofile
6.6 years ago zhao shilin ▴ 60
1
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4
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1.0k
views
Consensus sequence
Organism
updated 6.6 years ago by 14k • written 6.6 years ago by 56k
0
votes
0
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1.6k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
6.6 years ago Luo Weijun ★ 1.5k
0
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0
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1.0k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
6.6 years ago Guest User ★ 12k
0
votes
10
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872
views
Interspecies differential expression of orthologs with Edger
Normalization Organism edgeR
updated 6.6 years ago by ▴ 140 • written 6.6 years ago by 42k
0
votes
2
replies
666
views
Interspecies differential expression of orthologs with Edger
RNASeq Normalization Organism zebrafish edgeR
updated 6.6 years ago by 42k • written 6.6 years ago by ▴ 140
1
vote
3
replies
1.5k
views
Probeset/Transcript cluster definitions for HTA2.0 using pdInfoBuilder
BiocViews Annotation Organism biocViews pdInfoBuilder BiocViews BiocViews Annotation
updated 6.6 years ago by 56k • written 6.6 years ago by ▴ 40
0
votes
2
replies
915
views
Rebuild GO.sqlite from GO.db using complete GO database
Annotation GO Organism Annotation GO Organism
updated 6.7 years ago by ★ 7.2k • written 6.7 years ago by ▴ 40
0
votes
2
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1.6k
views
Genomic Features - makeTranscriptDbFromGFF()
Organism TranscriptDb GenomicFeatures Organism TranscriptDb GenomicFeatures
updated 6.8 years ago by ★ 7.2k • written 6.8 years ago by ★ 12k
0
votes
1
reply
751
views
Custom GeneSetCollection PFAM
Organism Organism
updated 6.9 years ago by 25k • written 6.9 years ago by ▴ 20
0
votes
2
replies
2.1k
views
DE analysis with reference transcriptome
Sequencing GO Organism edgeR DESeq EBSeq Sequencing GO Organism edgeR DESeq EBSeq
updated 6.9 years ago by 56k • written 6.9 years ago by ▴ 10
0
votes
3
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1.4k
views
DESeq/DESeq normalization on different experiments
Normalization Organism DESeq Normalization Organism DESeq
updated 6.9 years ago by 7.6k • written 6.9 years ago by ★ 12k
0
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0
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855
views
Please revise this edgeR code
Alignment Organism topGO edgeR Alignment Organism topGO edgeR
6.9 years ago biotech ▴ 160
0
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0
replies
952
views
Is this edgeR code OK?
Alignment Organism topGO edgeR Alignment Organism topGO edgeR
6.9 years ago biotech ▴ 160
0
votes
0
replies
1.4k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
7.0 years ago Elena Serrano ▴ 30
0
votes
1
reply
857
views
GOseq with ce6
GO Yeast Organism goseq genomes GO Yeast Organism goseq genomes
updated 7.0 years ago by ▴ 310 • written 7.0 years ago by ▴ 50
0
votes
1
reply
949
views
DEXSeq- dexseq_prepare_annotation.py error
Organism Organism
updated 7.0 years ago by ★ 3.6k • written 7.0 years ago by ▴ 140
0
votes
3
replies
1.8k
views
GOStats: summary hyperGTest, count and size
Annotation GO Organism GOstats Annotation GO Organism GOstats
7.1 years ago Christine Gläßer ▴ 60
0
votes
0
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1.5k
views
GOSeq with unsupported organism (Arabidopsis) and retrieving gene IDs from enriched GO categories
GO Organism PROcess goseq GO Organism PROcess goseq
7.1 years ago Dale Richardson ▴ 30
0
votes
2
replies
1.2k
views
TxDb file for Drerio (ie zebrafish)
Organism zebrafish CRISPRseek Organism zebrafish CRISPRseek
updated 7.1 years ago by 56k • written 7.1 years ago by ▴ 10
0
votes
5
replies
892
views
How does pathview deal with enzyme with several coding genes?
RNASeq Organism pathview RNASeq Organism pathview
7.2 years ago 刘鹏飞 ▴ 80
0
votes
7
replies
858
views
Gene Ontology Annotations from Gene Names
Microarray GO Organism PROcess GOstats Microarray GO Organism PROcess GOstats
updated 7.2 years ago by 56k • written 7.2 years ago by ★ 12k
0
votes
0
replies
684
views
Failure to Install Organism Package from AnnotationForge
Organism AnnotationDbi AnnotationForge Organism AnnotationDbi AnnotationForge
7.2 years ago Guest User ★ 12k
0
votes
1
reply
854
views
Using GOstats with ScanArray Express Data
Organism probe convert GOstats Organism probe convert GOstats
updated 7.2 years ago by 13k • written 7.2 years ago by ★ 12k
0
votes
0
replies
2.6k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
7.2 years ago Elena Serrano ▴ 30
0
votes
1
reply
565
views
forgeSeqFiles
Organism BSgenome BSgenome Organism BSgenome BSgenome
updated 7.3 years ago by 14k • written 7.3 years ago by ★ 12k
0
votes
1
reply
709
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges Rsubread easyRNASeq GO
updated 7.4 years ago by ▴ 320 • written 7.4 years ago by 42k
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0
replies
772
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
7.4 years ago Nicolas Delhomme ▴ 320
0
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1
reply
1.4k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
updated 7.4 years ago by ★ 4.3k • written 7.4 years ago by ▴ 270
0
votes
7
replies
1.3k
views
GTF file error when using easyRNAseq�
Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq
updated 7.4 years ago by ★ 1.2k • written 7.4 years ago by ★ 12k
0
votes
1
reply
1.0k
views
How to compare GO term lists and create matching network?
GO Network GUI Organism GO Network GUI Organism
updated 7.4 years ago by ▴ 750 • written 7.4 years ago by ▴ 160
0
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1
reply
1.0k
views
help: goseq and makeOrgPackageFromNCBI in AnnotationForge
RNASeq GO Organism AnnotationDbi goseq RNASeq GO Organism AnnotationDbi goseq
updated 7.4 years ago by ★ 7.2k • written 7.4 years ago by ▴ 80
0
votes
1
reply
819
views
Retrieve GO terms for organism without complete genomes and do enrichment by myself
GO Organism GO Organism
updated 7.4 years ago by ★ 7.2k • written 7.4 years ago by ▴ 110
0
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0
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708
views
Retrieve GO terms for unanontaded organism and do enrichment by myself
Proteomics GO Organism Proteomics GO Organism
7.5 years ago Ricardo Silva ▴ 110
1
vote
1
reply
1.2k
views
Mapping Affymetrix annotations with Bioconductor annotations
Annotation Organism zebrafish cdf affy AnnotationForge Annotation Organism zebrafish cdf
updated 7.5 years ago by 56k • written 7.5 years ago by ▴ 80
0
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0
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783
views
[devteam-bioc] Why does a GOAllFrame contain more rows than its argument GoFrame?
Annotation GO Organism AnnotationDbi Annotation GO Organism AnnotationDbi
7.5 years ago Marc Carlson ★ 7.2k
0
votes
1
reply
924
views
pathview
Organism convert pathview Organism convert pathview
updated 7.5 years ago by ★ 1.5k • written 7.5 years ago by ▴ 70
0
votes
1
reply
794
views
eayRNASeq with Ensemble GRCh37 help
Annotation Organism easyRNASeq DESeq2 Annotation Organism easyRNASeq DESeq2
updated 7.6 years ago by ★ 1.2k • written 7.6 years ago by ▴ 10
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0
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1.6k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
7.6 years ago Sarah Pohl ▴ 30
1
vote
3
replies
810
views
Bug in makeOrgPackageFromNCBI from AnnotationForge?
Alignment Annotation Organism Schizosaccharomyces pombe biomaRt AnnotationForge Alignment
updated 7.6 years ago by ★ 7.2k • written 7.6 years ago by ▴ 220
0
votes
0
replies
790
views
error while using goProfiles package on arabidopsis entrez gene IDs
GO Organism goProfiles GO Organism goProfiles
7.6 years ago Marc Carlson ★ 7.2k
0
votes
3
replies
651
views
defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package
Annotation GO Organism AnnotationDbi Annotation GO Organism AnnotationDbi
7.7 years ago Sashi ▴ 20
0
votes
1
reply
542
views
defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package
Annotation Organism AnnotationDbi Annotation Organism AnnotationDbi
updated 7.7 years ago by ★ 7.2k • written 7.7 years ago by ▴ 30
0
votes
0
replies
1.5k
views
topgo GO mapping for non model organisms
Annotation GO Organism topGO Annotation GO Organism topGO
7.7 years ago km ▴ 100
0
votes
1
reply
627
views
Error in .testGOFrame(x, organism) and invalid GO Evidence codes
GO Organism GO Organism
updated 7.7 years ago by ★ 7.2k • written 7.7 years ago by ▴ 10
0
votes
0
replies
1.9k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
7.7 years ago Luo Weijun ★ 1.5k
0
votes
0
replies
1.3k
views
Pathview with non-KEGG organisms?
Pathways Organism pathview Pathways Organism pathview
7.7 years ago Luo Weijun ★ 1.5k
0
votes
3
replies
823
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
7.7 years ago Alan Smith ▴ 150
0
votes
4
replies
782
views
FeatureExpressionSet using list.files() in place of read.xysfiles()
Microarray Annotation GO Organism probe annotate limma convert pdInfoBuilder sva GO sva
updated 7.8 years ago by ★ 4.3k • written 7.8 years ago by ▴ 140
218 results • Page 1 of 5
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Answer: DepMap copy number by Laurent Gatto 1.5k
Hi Danny - sorry for the delay in answering, I hadn't set `depmap` as a tag yet. Yes, that bug has been fixed in the devel version.
Answer: High fold change reported for comparison of samples with zero values in all samp by James W. MacDonald 56k
The universal recommendation is to remove all genes with consistently low (or all zero) expression values prior to doing any modeling. It i…
Comment: Sample quality weights for RNA-seq by Naomi Altman ★ 6.0k
Thanks Michael. I'll try that. (Limma folks, I'd still love to hear from you.)
Answer: Installation error if message implemented in .Rprofile by Mike Smith ★ 4.9k
A similar issue has been reported recently for rhdf5filters (https://github.com/grimbough/rhdf5filters/issues/11) and rhdf5 (https://github…
Comment: Couldn't load org.Hs.eg.db by Xulei Huo • 0
That does not work, i have tried it.
Votes
Answer: TargetsFile. Where it is?
Answer: TargetsFile. Where it is?
Comment: TargetsFile. Where it is?
Comment: Using DESeq2 to identify changing transcriptional activity in a metagenome
Answer: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
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