Showing : organism • reset
0
votes
4
replies
8.1k
views
DESeq adjusted pvalue calculation / filtering data
Sequencing Organism qvalue DESeq Sequencing Organism qvalue DESeq
updated 12.4 years ago by ★ 6.0k • written 12.4 years ago by ▴ 20
0
votes
4
replies
4.3k
views
An error in oligo: All the CEL files must be of the same type??
BiocViews Annotation Organism biocViews oligo BiocViews BiocViews Annotation Organism
updated 12.9 years ago by ★ 4.3k • written 12.9 years ago by ▴ 20
0
votes
0
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3.4k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.2 years ago Elena Serrano ▴ 30
0
votes
10
replies
3.0k
views
PAIR files -- feature set table
Microarray Annotation Organism annotate pdInfoBuilder Microarray Annotation Organism
updated 10.9 years ago by ★ 4.3k • written 10.9 years ago by ★ 13k
0
votes
13
replies
2.8k
views
GEOmetadb and gse organism type
Cancer Breast Organism GEOmetadb Cancer Breast Organism GEOmetadb
updated 15.1 years ago by 21k • written 15.1 years ago by ▴ 180
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
10
replies
2.8k
views
gene set enrichment
Annotation Organism Annotation Organism
updated 2.1 years ago by 50k • written 11.4 years ago by ▴ 220
2
votes
4
replies
2.6k
views
makePdInfoPackage for Primeview arrays
BiocViews Annotation Cancer Organism cdf probe affy biocViews BiocViews BiocViews Cancer
updated 10.8 years ago by ★ 3.9k • written 10.8 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
2.6k
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
7
replies
2.6k
views
GTF file error when using easyRNAseq�
Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq
updated 10.4 years ago by ★ 1.2k • written 10.4 years ago by ★ 13k
0
votes
2
replies
2.5k
views
annotation and GO for non-model organism
Microarray Annotation GO Organism Microarray Annotation GO Organism
updated 14.6 years ago by ★ 7.2k • written 14.6 years ago by ▴ 150
0
votes
2
replies
2.4k
views
Problem in SPIA: de must be a vector of log2 fold changes. The names of de should be included in the refference array!
Organism limma SPIA Organism limma SPIA
updated 12.3 years ago by ▴ 570 • written 12.3 years ago by ▴ 100
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
replies
2.4k
views
Genomic Features - makeTranscriptDbFromGFF()
Organism TranscriptDb GenomicFeatures Organism TranscriptDb GenomicFeatures
updated 9.8 years ago by ★ 7.2k • written 9.9 years ago by ★ 13k
0
votes
1
reply
2.3k
views
PFAM gene enrichment test using GOstats and Category
Annotation GO Organism GOstats Category Annotation GO Organism GOstats Category
updated 12.4 years ago by ★ 7.2k • written 12.4 years ago by ▴ 10
0
votes
0
replies
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
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
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
2.2k
views
Bioconductor Digest, Vol 120, Issue 12
Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy
11.2 years ago Matthew Thornton ▴ 350
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
0
votes
3
replies
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
2.1k
views
Pathview with non-KEGG organisms?
Pathways Organism pathview Pathways Organism pathview
10.7 years ago Luo Weijun ★ 1.6k
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
2
votes
3
replies
2.1k
views
How to get position for each gene ID/gene symbol instead of position for each transcript
Organism PROcess biomaRt GenomicFeatures Organism PROcess biomaRt GenomicFeatures
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ★ 1.0k
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
0
replies
2.0k
views
vacancy postdoc or PhD in the Netherlands
Metabolomics Network Organism Metabolomics Network Organism
15.1 years ago Hendriks, M. ▴ 10
0
votes
8
replies
2.0k
views
AnnBuilder and Kegg
Pathways GO Survival Cancer Organism annotate affydata vsn AnnBuilder globaltest GO vsn
updated 17.4 years ago by ▴ 190 • written 17.4 years ago by ★ 2.9k
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
1.9k
views
GWASTools
Organism GWASTools Organism GWASTools SNPRelate
11.1 years ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
1.8k
views
Compressed boxplots after 'normexp+offset' background correction of Agilent one color microarrays in LIMMA
Normalization Organism limma Normalization Organism limma
updated 11.8 years ago by ★ 2.0k • written 11.8 years ago by ▴ 10
1
vote
1
reply
1.8k
views
Mapping Affymetrix annotations with Bioconductor annotations
Annotation Organism zebrafish cdf affy AnnotationForge Annotation Organism zebrafish cdf
updated 10.5 years ago by 65k • written 10.5 years ago by ▴ 80
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
4
replies
1.8k
views
KEGGgraph
Pathways Organism graph PROcess KEGGgraph Pathways Organism graph PROcess KEGGgraph
11.5 years ago Ricardo Silva ▴ 110
1
vote
4
replies
1.8k
views
Consensus sequence
Organism
updated 9.6 years ago by 16k • written 9.6 years ago by 65k
0
votes
1
reply
1.8k
views
Bioconductor Digest, Vol 115, Issue 22
Transcription Sequencing miRNA SmallRNA Annotation Normalization GO Cancer Organism edgeR
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ▴ 10
0
votes
2
replies
1.8k
views
pdInfoBuilder fails on Affy's GeneChip Human Transcriptome Array 2.0
BiocViews Annotation Organism biocViews oligo oligoClasses BiocViews BiocViews Annotation
updated 8.9 years ago by ▴ 20 • written 10.2 years ago by ▴ 40
0
votes
0
replies
1.8k
views
BioNet - interpretation of node score (Eva Benito Garagorri)
SNP Microarray GO Network Clustering Cancer Organism mgug4122a probe limma convert SNP
13.6 years ago Daniela Beißer ▴ 20
0
votes
0
replies
1.8k
views
Median-Interquartile Normalization
Microarray SystemsBiology Annotation GO Preprocessing Clustering Cancer Yeast Organism GO
16.5 years ago McGee, Monnie ▴ 300
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
1
reply
1.7k
views
How to compare GO term lists and create matching network?
GO Network GUI Organism GO Network GUI Organism
updated 10.4 years ago by ▴ 750 • written 10.4 years ago by ▴ 160
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
3
replies
1.7k
views
Fwd: Re: which package can do GSEA for no model organism
Annotation GO Organism ASSIGN Annotation GO Organism ASSIGN
updated 14.8 years ago by ▴ 40 • written 14.8 years ago by ▴ 340
0
votes
4
replies
1.7k
views
easyRNASeq error
Sequencing Alignment Annotation Organism BSgenome biomaRt BSgenome easyRNASeq Sequencing
12.1 years ago delhomme@embl.de ★ 1.2k
0
votes
3
replies
1.7k
views
BLAST - annotate package?
Organism Organism
updated 11.6 years ago by 65k • written 11.6 years ago by ★ 1.1k
0
votes
0
replies
1.7k
views
SPIA algorithm organisms not included already in the SPIA package
Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST
11.1 years ago Tarca, Adi ▴ 570
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
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
votes
1
reply
1.6k
views
problem creating own org.Ss.eg.db
Annotation GO Organism OrgDb Annotation GO Organism OrgDb
updated 12.1 years ago by ★ 3.9k • written 12.1 years ago by ★ 7.2k
0
votes
2
replies
1.6k
views
Flanking TSS region for reverse strand using biomaRt
Yeast Organism biomaRt Yeast Organism biomaRt
updated 13.4 years ago by ▴ 10 • written 13.4 years ago by ▴ 340
50 results • Page 1 of 1
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Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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