Showing : organism • reset
1
vote
8
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1.6k
views
Non-model organism , CluserProfiler message "No gene can be mapped"
organism non-model
updated 2.1 years ago by 67k • written 2.1 years ago by • 0
0
votes
2
replies
2.0k
views
pdInfoBuilder fails on Affy's GeneChip Human Transcriptome Array 2.0
BiocViews Annotation Organism biocViews oligo oligoClasses BiocViews BiocViews Annotation
updated 9.5 years ago by ▴ 20 • written 10.8 years ago by ▴ 40
0
votes
0
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1.7k
views
Re: KEGGprofile: "Error in phyper - Non-numeric argument to mathematical function" when using non model organism
Organism KEGGprofile
10.2 years ago zhao shilin ▴ 60
1
vote
4
replies
2.0k
views
Consensus sequence
Organism
updated 10.2 years ago by 16k • written 10.2 years ago by 67k
0
votes
0
replies
2.4k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
10.2 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.8k
views
Gostats Hypergeometric tests for non model organisms Kegg pathway
Pathways GO Organism GOstats
10.2 years ago Guest User ★ 13k
0
votes
10
replies
2.1k
views
Interspecies differential expression of orthologs with Edger
Normalization Organism edgeR
updated 10.2 years ago by ▴ 140 • written 10.2 years ago by 51k
0
votes
2
replies
1.3k
views
Interspecies differential expression of orthologs with Edger
RNASeq Normalization Organism zebrafish edgeR
updated 10.2 years ago by 51k • written 10.2 years ago by ▴ 140
1
vote
3
replies
2.6k
views
Probeset/Transcript cluster definitions for HTA2.0 using pdInfoBuilder
BiocViews Annotation Organism biocViews pdInfoBuilder BiocViews BiocViews Annotation
updated 10.2 years ago by 67k • written 10.2 years ago by ▴ 40
0
votes
2
replies
1.5k
views
Rebuild GO.sqlite from GO.db using complete GO database
Annotation GO Organism Annotation GO Organism
updated 10.3 years ago by ★ 7.2k • written 10.3 years ago by ▴ 40
0
votes
2
replies
2.5k
views
Genomic Features - makeTranscriptDbFromGFF()
Organism TranscriptDb GenomicFeatures Organism TranscriptDb GenomicFeatures
updated 10.4 years ago by ★ 7.2k • written 10.4 years ago by ★ 13k
0
votes
1
reply
1.2k
views
Custom GeneSetCollection PFAM
Organism Organism
updated 10.4 years ago by 25k • written 10.4 years ago by ▴ 20
0
votes
2
replies
3.1k
views
DE analysis with reference transcriptome
Sequencing GO Organism edgeR DESeq EBSeq Sequencing GO Organism edgeR DESeq EBSeq
updated 10.5 years ago by 67k • written 10.5 years ago by ▴ 10
0
votes
3
replies
2.3k
views
DESeq/DESeq normalization on different experiments
Normalization Organism DESeq Normalization Organism DESeq
updated 10.5 years ago by ★ 7.9k • written 10.5 years ago by ★ 13k
0
votes
0
replies
1.4k
views
Please revise this edgeR code
Alignment Organism topGO edgeR Alignment Organism topGO edgeR
10.5 years ago biotech ▴ 160
0
votes
0
replies
1.6k
views
Is this edgeR code OK?
Alignment Organism topGO edgeR Alignment Organism topGO edgeR
10.5 years ago biotech ▴ 160
0
votes
0
replies
2.3k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.6 years ago Elena Serrano ▴ 30
0
votes
1
reply
1.7k
views
GOseq with ce6
GO Yeast Organism goseq genomes GO Yeast Organism goseq genomes
updated 10.6 years ago by ▴ 320 • written 10.6 years ago by ▴ 50
0
votes
1
reply
1.6k
views
DEXSeq- dexseq_prepare_annotation.py error
Organism Organism
updated 10.6 years ago by ★ 3.8k • written 10.6 years ago by ▴ 140
0
votes
3
replies
2.8k
views
GOStats: summary hyperGTest, count and size
Annotation GO Organism GOstats Annotation GO Organism GOstats
10.7 years ago Christine Gläßer ▴ 60
0
votes
0
replies
2.4k
views
GOSeq with unsupported organism (Arabidopsis) and retrieving gene IDs from enriched GO categories
GO Organism PROcess goseq GO Organism PROcess goseq
10.7 years ago Dale Richardson ▴ 30
0
votes
2
replies
2.0k
views
TxDb file for Drerio (ie zebrafish)
Organism zebrafish CRISPRseek Organism zebrafish CRISPRseek
updated 10.7 years ago by 67k • written 10.7 years ago by ▴ 10
0
votes
5
replies
1.8k
views
How does pathview deal with enzyme with several coding genes?
RNASeq Organism pathview RNASeq Organism pathview
10.7 years ago 刘鹏飞 ▴ 80
0
votes
7
replies
2.2k
views
Gene Ontology Annotations from Gene Names
Microarray GO Organism PROcess GOstats Microarray GO Organism PROcess GOstats
updated 10.8 years ago by 67k • written 10.8 years ago by ★ 13k
0
votes
0
replies
1.3k
views
Failure to Install Organism Package from AnnotationForge
Organism AnnotationDbi AnnotationForge Organism AnnotationDbi AnnotationForge
10.8 years ago Guest User ★ 13k
0
votes
1
reply
1.6k
views
Using GOstats with ScanArray Express Data
Organism probe convert GOstats Organism probe convert GOstats
updated 10.8 years ago by ★ 13k • written 10.8 years ago by ★ 13k
0
votes
0
replies
3.6k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.8 years ago Elena Serrano ▴ 30
0
votes
1
reply
997
views
forgeSeqFiles
Organism BSgenome BSgenome Organism BSgenome BSgenome
updated 10.9 years ago by 16k • written 10.9 years ago by ★ 13k
0
votes
1
reply
1.5k
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 11.0 years ago by ▴ 320 • written 11.0 years ago by 51k
0
votes
0
replies
1.3k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
11.0 years ago Nicolas Delhomme ▴ 320
0
votes
1
reply
2.2k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
updated 11.0 years ago by ★ 4.3k • written 11.0 years ago by ▴ 290
0
votes
7
replies
3.0k
views
GTF file error when using easyRNAseq�
Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq
updated 11.0 years ago by ★ 1.2k • written 11.0 years ago by ★ 13k
0
votes
1
reply
1.9k
views
How to compare GO term lists and create matching network?
GO Network GUI Organism GO Network GUI Organism
updated 11.0 years ago by ▴ 750 • written 11.0 years ago by ▴ 160
0
votes
1
reply
1.7k
views
help: goseq and makeOrgPackageFromNCBI in AnnotationForge
RNASeq GO Organism AnnotationDbi goseq RNASeq GO Organism AnnotationDbi goseq
updated 11.0 years ago by ★ 7.2k • written 11.0 years ago by ▴ 80
0
votes
1
reply
1.3k
views
Retrieve GO terms for organism without complete genomes and do enrichment by myself
GO Organism GO Organism
updated 11.0 years ago by ★ 7.2k • written 11.0 years ago by ▴ 110
0
votes
0
replies
1.2k
views
Retrieve GO terms for unanontaded organism and do enrichment by myself
Proteomics GO Organism Proteomics GO Organism
11.0 years ago Ricardo Silva ▴ 110
1
vote
1
reply
1.9k
views
Mapping Affymetrix annotations with Bioconductor annotations
Annotation Organism zebrafish cdf affy AnnotationForge Annotation Organism zebrafish cdf
updated 11.1 years ago by 67k • written 11.1 years ago by ▴ 80
0
votes
0
replies
1.3k
views
[devteam-bioc] Why does a GOAllFrame contain more rows than its argument GoFrame?
Annotation GO Organism AnnotationDbi Annotation GO Organism AnnotationDbi
11.1 years ago Marc Carlson ★ 7.2k
0
votes
1
reply
2.0k
views
pathview
Organism convert pathview Organism convert pathview
updated 11.1 years ago by ★ 1.6k • written 11.1 years ago by ▴ 70
0
votes
1
reply
1.5k
views
eayRNASeq with Ensemble GRCh37 help
Annotation Organism easyRNASeq DESeq2 Annotation Organism easyRNASeq DESeq2
updated 11.2 years ago by ★ 1.2k • written 11.2 years ago by ▴ 10
0
votes
0
replies
2.3k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
11.2 years ago Sarah Pohl ▴ 30
1
vote
3
replies
1.9k
views
Bug in makeOrgPackageFromNCBI from AnnotationForge?
Alignment Annotation Organism Schizosaccharomyces pombe biomaRt AnnotationForge Alignment
updated 11.2 years ago by ★ 7.2k • written 11.2 years ago by ▴ 220
0
votes
0
replies
1.4k
views
error while using goProfiles package on arabidopsis entrez gene IDs
GO Organism goProfiles GO Organism goProfiles
11.2 years ago Marc Carlson ★ 7.2k
0
votes
3
replies
1.3k
views
defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package
Annotation GO Organism AnnotationDbi Annotation GO Organism AnnotationDbi
11.3 years ago • updated 11.2 years ago Sashi ▴ 20
0
votes
1
reply
1.1k
views
defining accessors (cols, keys, keytypes, select) for annotation package built with AnnotationForge package
Annotation Organism AnnotationDbi Annotation Organism AnnotationDbi
updated 11.3 years ago by ★ 7.2k • written 11.3 years ago by ▴ 30
0
votes
0
replies
2.4k
views
topgo GO mapping for non model organisms
Annotation GO Organism topGO Annotation GO Organism topGO
11.3 years ago km ▴ 100
0
votes
1
reply
1.3k
views
Error in .testGOFrame(x, organism) and invalid GO Evidence codes
GO Organism GO Organism
updated 11.3 years ago by ★ 7.2k • written 11.3 years ago by ▴ 10
0
votes
0
replies
2.8k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
11.3 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
2.3k
views
Pathview with non-KEGG organisms?
Pathways Organism pathview Pathways Organism pathview
11.3 years ago Luo Weijun ★ 1.6k
0
votes
3
replies
1.6k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
11.3 years ago Alan Smith ▴ 150
50 results • Page 1 of 1
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Comment: Appropriate ways to filter counts data for voom/limma by dorothylminter • 0
The proper way to filter count data for voom/limma emphasizes the importance of choosing the right filtering technique to enhance detection…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by Robert Castelo ★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Comment: DESeq2 rerun returns different results by ATpoint ★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
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A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
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