Showing : organism • reset
0
votes
8
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1.2k
views
Non-model organism , CluserProfiler message "No gene can be mapped"
organism non-model
updated 19 months ago by 65k • written 19 months ago by • 0
0
votes
2
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1.8k
views
pdInfoBuilder fails on Affy's GeneChip Human Transcriptome Array 2.0
BiocViews Annotation Organism biocViews oligo oligoClasses BiocViews BiocViews Annotation
updated 9.0 years ago by ▴ 20 • written 10.3 years ago by ▴ 40
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1.5k
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Re: KEGGprofile: "Error in phyper - Non-numeric argument to mathematical function" when using non model organism
Organism KEGGprofile
9.6 years ago zhao shilin ▴ 60
1
vote
4
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1.8k
views
Consensus sequence
Organism
updated 9.6 years ago by 16k • written 9.6 years ago by 65k
0
votes
0
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2.3k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
9.6 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.7k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
9.6 years ago Guest User ★ 13k
0
votes
10
replies
1.8k
views
Interspecies differential expression of orthologs with Edger
Normalization Organism edgeR
updated 9.6 years ago by ▴ 140 • written 9.6 years ago by 50k
0
votes
2
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1.1k
views
Interspecies differential expression of orthologs with Edger
RNASeq Normalization Organism zebrafish edgeR
updated 9.6 years ago by 50k • written 9.6 years ago by ▴ 140
1
vote
3
replies
2.4k
views
Probeset/Transcript cluster definitions for HTA2.0 using pdInfoBuilder
BiocViews Annotation Organism biocViews pdInfoBuilder BiocViews BiocViews Annotation
updated 9.7 years ago by 65k • written 9.7 years ago by ▴ 40
0
votes
2
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1.4k
views
Rebuild GO.sqlite from GO.db using complete GO database
Annotation GO Organism Annotation GO Organism
updated 9.8 years ago by ★ 7.2k • written 9.8 years ago by ▴ 40
0
votes
2
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2.4k
views
Genomic Features - makeTranscriptDbFromGFF()
Organism TranscriptDb GenomicFeatures Organism TranscriptDb GenomicFeatures
updated 9.9 years ago by ★ 7.2k • written 9.9 years ago by ★ 13k
0
votes
1
reply
1.1k
views
Custom GeneSetCollection PFAM
Organism Organism
updated 9.9 years ago by 25k • written 9.9 years ago by ▴ 20
0
votes
2
replies
2.8k
views
DE analysis with reference transcriptome
Sequencing GO Organism edgeR DESeq EBSeq Sequencing GO Organism edgeR DESeq EBSeq
updated 9.9 years ago by 65k • written 9.9 years ago by ▴ 10
0
votes
3
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2.1k
views
DESeq/DESeq normalization on different experiments
Normalization Organism DESeq Normalization Organism DESeq
updated 9.9 years ago by ★ 7.9k • written 9.9 years ago by ★ 13k
0
votes
0
replies
1.3k
views
Please revise this edgeR code
Alignment Organism topGO edgeR Alignment Organism topGO edgeR
10.0 years ago biotech ▴ 160
0
votes
0
replies
1.4k
views
Is this edgeR code OK?
Alignment Organism topGO edgeR Alignment Organism topGO edgeR
10.0 years ago biotech ▴ 160
0
votes
0
replies
2.1k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.0 years ago Elena Serrano ▴ 30
0
votes
1
reply
1.5k
views
GOseq with ce6
GO Yeast Organism goseq genomes GO Yeast Organism goseq genomes
updated 10.0 years ago by ▴ 310 • written 10.0 years ago by ▴ 50
0
votes
1
reply
1.5k
views
DEXSeq- dexseq_prepare_annotation.py error
Organism Organism
updated 10.0 years ago by ★ 3.7k • written 10.0 years ago by ▴ 140
0
votes
3
replies
2.6k
views
GOStats: summary hyperGTest, count and size
Annotation GO Organism GOstats Annotation GO Organism GOstats
10.1 years ago Christine Gläßer ▴ 60
0
votes
0
replies
2.2k
views
GOSeq with unsupported organism (Arabidopsis) and retrieving gene IDs from enriched GO categories
GO Organism PROcess goseq GO Organism PROcess goseq
10.1 years ago Dale Richardson ▴ 30
0
votes
2
replies
1.8k
views
TxDb file for Drerio (ie zebrafish)
Organism zebrafish CRISPRseek Organism zebrafish CRISPRseek
updated 10.2 years ago by 65k • written 10.2 years ago by ▴ 10
0
votes
5
replies
1.6k
views
How does pathview deal with enzyme with several coding genes?
RNASeq Organism pathview RNASeq Organism pathview
10.2 years ago 刘鹏飞 ▴ 80
0
votes
7
replies
1.9k
views
Gene Ontology Annotations from Gene Names
Microarray GO Organism PROcess GOstats Microarray GO Organism PROcess GOstats
updated 10.2 years ago by 65k • written 10.2 years ago by ★ 13k
0
votes
0
replies
1.2k
views
Failure to Install Organism Package from AnnotationForge
Organism AnnotationDbi AnnotationForge Organism AnnotationDbi AnnotationForge
10.2 years ago Guest User ★ 13k
0
votes
1
reply
1.4k
views
Using GOstats with ScanArray Express Data
Organism probe convert GOstats Organism probe convert GOstats
updated 10.2 years ago by ★ 13k • written 10.2 years ago by ★ 13k
0
votes
0
replies
3.4k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.3 years ago Elena Serrano ▴ 30
0
votes
1
reply
908
views
forgeSeqFiles
Organism BSgenome BSgenome Organism BSgenome BSgenome
updated 10.3 years ago by 16k • written 10.3 years ago by ★ 13k
0
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1
reply
1.3k
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 10.4 years ago by ▴ 320 • written 10.4 years ago by 50k
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0
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1.2k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
10.4 years ago Nicolas Delhomme ▴ 320
0
votes
1
reply
2.0k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
updated 10.4 years ago by ★ 4.3k • written 10.4 years ago by ▴ 290
0
votes
7
replies
2.6k
views
GTF file error when using easyRNAseq�
Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq
updated 10.5 years ago by ★ 1.2k • written 10.5 years ago by ★ 13k
0
votes
1
reply
1.7k
views
How to compare GO term lists and create matching network?
GO Network GUI Organism GO Network GUI Organism
updated 10.5 years ago by ▴ 750 • written 10.5 years ago by ▴ 160
0
votes
1
reply
1.5k
views
help: goseq and makeOrgPackageFromNCBI in AnnotationForge
RNASeq GO Organism AnnotationDbi goseq RNASeq GO Organism AnnotationDbi goseq
updated 10.5 years ago by ★ 7.2k • written 10.5 years ago by ▴ 80
0
votes
1
reply
1.2k
views
Retrieve GO terms for organism without complete genomes and do enrichment by myself
GO Organism GO Organism
updated 10.5 years ago by ★ 7.2k • written 10.5 years ago by ▴ 110
0
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0
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1.1k
views
Retrieve GO terms for unanontaded organism and do enrichment by myself
Proteomics GO Organism Proteomics GO Organism
10.5 years ago Ricardo Silva ▴ 110
1
vote
1
reply
1.8k
views
Mapping Affymetrix annotations with Bioconductor annotations
Annotation Organism zebrafish cdf affy AnnotationForge Annotation Organism zebrafish cdf
updated 10.6 years ago by 65k • written 10.6 years ago by ▴ 80
0
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0
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1.2k
views
[devteam-bioc] Why does a GOAllFrame contain more rows than its argument GoFrame?
Annotation GO Organism AnnotationDbi Annotation GO Organism AnnotationDbi
10.6 years ago Marc Carlson ★ 7.2k
0
votes
1
reply
1.7k
views
pathview
Organism convert pathview Organism convert pathview
updated 10.6 years ago by ★ 1.6k • written 10.6 years ago by ▴ 70
0
votes
1
reply
1.3k
views
eayRNASeq with Ensemble GRCh37 help
Annotation Organism easyRNASeq DESeq2 Annotation Organism easyRNASeq DESeq2
updated 10.6 years ago by ★ 1.2k • written 10.6 years ago by ▴ 10
0
votes
0
replies
2.2k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
10.7 years ago Sarah Pohl ▴ 30
1
vote
3
replies
1.7k
views
Bug in makeOrgPackageFromNCBI from AnnotationForge?
Alignment Annotation Organism Schizosaccharomyces pombe biomaRt AnnotationForge Alignment
updated 10.7 years ago by ★ 7.2k • written 10.7 years ago by ▴ 220
0
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0
replies
1.2k
views
error while using goProfiles package on arabidopsis entrez gene IDs
GO Organism goProfiles GO Organism goProfiles
10.7 years ago Marc Carlson ★ 7.2k
0
votes
3
replies
1.2k
views
defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package
Annotation GO Organism AnnotationDbi Annotation GO Organism AnnotationDbi
10.7 years ago Sashi ▴ 20
0
votes
1
reply
977
views
defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package
Annotation Organism AnnotationDbi Annotation Organism AnnotationDbi
updated 10.7 years ago by ★ 7.2k • written 10.7 years ago by ▴ 30
0
votes
0
replies
2.2k
views
topgo GO mapping for non model organisms
Annotation GO Organism topGO Annotation GO Organism topGO
10.7 years ago km ▴ 100
0
votes
1
reply
1.1k
views
Error in .testGOFrame(x, organism) and invalid GO Evidence codes
GO Organism GO Organism
updated 10.7 years ago by ★ 7.2k • written 10.7 years ago by ▴ 10
0
votes
0
replies
2.6k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
10.7 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
2.1k
views
Pathview with non-KEGG organisms?
Pathways Organism pathview Pathways Organism pathview
10.8 years ago Luo Weijun ★ 1.6k
0
votes
3
replies
1.5k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
10.8 years ago Alan Smith ▴ 150
50 results • Page 1 of 1
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Replies
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by Guangchuang Yu ★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference by ATpoint ★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
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